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Anion-Mediated Fe3+ Release Mechanism in Ovotransferrin C-Lobe: a Structurally

Identified SO42- Binding Site and its Implications for the Kinetic Pathway†‡

†This work was supported in part by a grant-in-aid for scientific research from the Ministry of

Education, Science, Sports and Culture of Japan.

‡The atomic coordinate of the apo structure has been deposited as the entry number 1IQ7

with the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers

University, New Brunswick, NJ (http://www.rcsb.org/).

Kimihiko Mizutani,#§ B.K. Muralidhara, #§ Honami Yamashita, Satoshi Tabata,

Bunzo Mikami,§ and Masaaki Hirose*§

The Research Institute for Food Science, Kyoto University, Uji, Kyoto 611 0011, Japan

#K.M. and B.K.M. equally contributed to this work.

*To whom correspondence should be addressed.

Tel: 81-774-38-3734; Fax: 81-774-38-3735; e-mail: hirose@soya.food.kyoto-u.ac.jp

The Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611 0011, Japan

§Present address: The Graduate School of Agriculture, Kyoto University, Uji, Kyoto 6110011,

Japan for K. M., B. M., and M. H., and Department of Protein Chemistry and Technology,

Central Food Technological Research Institute, Mysore 570013, India for B. K. M.

Copyright 2001 by The American Society for Biochemistry and Molecular Biology, Inc.

JBC Papers in Press. Published on July 20, 2001 as Manuscript M102590200 by guest on O

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RUNNING TITLE: Iron Release Mechanism in Ovotransferrin C-Lobe

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SUMMARY: The differential properties of anion-mediated Fe3+-release between the N- and

C-lobes of transferrins have been a focus in transferrin biochemistry. The structural and

kinetic characteristics for isolated lobe have, however, been documented with the N-lobe only.

Here we demonstrate for the first time the quantitative Fe3+-release kinetics and the

anion-binding structure for the isolated C-lobe of ovotransferrin. In presence of

pyrophosphate, sulfate, and nitrilotriacetate anions, the C-lobe released Fe3+ with a

decelerated rate in a single exponential progress curve, and the observed first-order rate

constants displayed a hyperbolic profile as a function of the anion concentration. The profile

was consistent with a newly derived single-pathway Fe3+ release model in which the holo

form is converted depending on the anion concentration into a ‘mixed-ligand’ intermediate

that releases Fe3+. The apo C-lobe was crystallized in ammonium sulfate solution and the

structure determined at 2.3 Å resolution demonstrated the existence of a single bound SO42-

in the interdomain cleft, which interacts directly with Thr 461-OG1, Tyr 431-OH, and His

592-NE2, and indirectly with Tyr 524-OH. The latter three groups are Fe3+-coordinating

ligands, strongly suggesting the facilitated Fe3+-release upon the anion occupation at this site.

The SO42- binding structure supported the single-pathway kinetic model.

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INTRODUCTION

Transferrins are a homologous group of iron-binding proteins that include serum

transferrin, ovotransferrin and lactoferrin (1). These proteins are ~80 kDa single chain

proteins and have the ability to bind very tightly, but reversibly, two Fe3+ together with two

CO32- anions (1). Serum transferrin is the Fe3+-transporter protein that mediates the delivery

of Fe3+ from blood to the target cells. Ovotransferrin, a major egg-white protein, should share

the same structural characteristics as hen serum transferrin, since these proteins are derived

from the same gene and differ only in their attached carbohydrate (2). Furthermore, several

lines of in vitro evidence have demonstrated that ovotransferrin possesses the cellular Fe3+

transport function (3-5), although the in vivo transport function in the developing egg has not

been proved for this egg white protein. In contrast, lactoferrin is a non- Fe3+-transporter

protein and has a variety of biological functions, including an antimicrobial activity (6) and a

sequence-specific DNA binding capacity (7). The Fe3+ -transporter transferrins mediate the

delivery of Fe3+ to the target cells through the interaction with the specific transferrin

receptor; the Fe3+-loaded transferrins are first bound by the receptor on the plasma membrane,

and then internalized by the cell into the endosome where Fe3+ release takes place in an

acidic environment (8). In vitro, the release of Fe3+ from ferric transferrins requires the

presence of a simple anion, such as pyrophosphate, sulfate, and chloride (9-13). The

requirement of anion for the Fe3+ release has been also demonstrated for the

Fe3+-transferrin-receptor complex (14), indicating the implications of some anion for the

cellular Fe3+ release.

The transferrin molecule consists of two homologous N- and C-lobes, and these lobes

are further divided into two similarly sized domains (domains 1 and 2). The two iron-binding

sites are located within the interdomain cleft of each lobe. From the crystal structures of the

diferric forms (15-20) and the monoferric N-lobes (21-24) of several transferrins, it has been

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shown that the two domains of each lobe are closed over an Fe3+ ion. Out of the six

coordination sites of Fe3+, four are occupied by protein ligands (2 Tyr, 1 Asp and 1 His

residues) and the other two by a bidentate carbonate anion. In the Fe3+-free apo form, both

the lobes of ovotransferrin and serum transferrin assume a conformation with an opening of

the interdomain cleft, as revealed by X-ray crystallographic (25-27) and solution scattering

(28-31) analyses. The anion-induced Fe3+ release by transferrins, therefore, should be closely

related to the opening of the domains in either lobe.

Upon the transition from the closed to open conformation, the two domains of the N- and

C-lobes behave as rigid bodies and the conformational change almost lies in the hinge

regions that link the two domains (32, 33). Such a mode of conformational transition in

transferrins has been pointed out to be a typical example of the hinge motion mechanism in

multidomain proteins that undergo significant conformational transition upon exertion of the

biologically important functions (34). When the functional characteristics are compared for

the N- and C-lobes of transferrins, the effects of anions on the Fe3+ release kinetics are

strikingly different for the two lobes. The rate for the anion-mediated Fe3+ release is much

slower from the C-lobe than from the N-lobe (35-37) and a kinetically significant anion

binding (KISAB) site that has been proposed for the C-lobe as the binding site of a variety of

simple anions is not kinetically detected for the N-lobe (38). Detailed structural and

functional comparisons between the N- and C-lobes of transferrins may provide crucial

information about the hinge motion mechanism of biologically important multidomain

proteins.

As a promising strategy for understanding the structural and functional differences, direct

comparison between the isolated N- and C-lobes in terms of the crystal structure and

quantitative Fe3+-release kinetics should be crucial. There is, however, no report about the

crystal structure or Fe3+-release kinetics for the isolated C-lobe, despite a large number of

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publications for the isolated N-lobes (21-24, 39-43). This is probably due to the absence of an

efficient C-lobe recombinant expression system and to the difficulty in its proteolytic

isolation from whole transferrin molecule except for ovotransferrin (44). Furthermore, few

attempts have been made to figure out a model for the Fe3+ release pathway on the basis of a

quantitative kinetic analysis and to correlate the obtained kinetic pathway with the anion

binding structure.

In the present paper, we demonstrate, for the first time, the X-ray crystallographic

structure and the results from quantitative kinetic analyses for an isolated C-lobe. The

anion-dependent Fe3+ release from C-oTf1 at the endosomal pH 5.6 follows a single

exponential progress curve, and the obtained apparent first-order rate constants display a

hyperbolic profile as a function of anion concentrations. From the curve-fitting analysis for

the profile using a quantitative rate equation, a single Fe3+-release pathway model is found to

be the most feasible one; in this model, the holo form is converted depending on the anion

concentration into a ‘mixed-ligand’ intermediate that releases Fe3+. To evaluate this kinetic

model on the structural basis, C-oTf has been crystallized as the apo form in ammonium

sulfate solution and solved for its three-dimensional structure at 2.3 Å resolution. The solved

structure represents the existence of a single bound SO42- with reasonably low B-factors in

the opened interdomain clef; the bound SO42- interacts directly with Thr 461-OG1, Tyr

431-OH, and His 592-NE2, and indirectly with Tyr 524-OH. The latter three residue groups

correspond to Fe3+-coordinating ligands, strongly suggesting the facilitated Fe3+-release upon

the anion occupation for the site. The structural characteristics of the SO42- binding site can

be successfully used to support and substantiate the single-pathway kinetic model. Taken

together with previous crystallographic (39) and kinetic (43) data for isolated ovotransferrin

N-lobe, the present data for C-oTf should provide crucial information about structural

implications for the functional difference in the N- and C-lobes of transferrins.

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EXPERIMENTAL PROCEDURES

Materials. C-oTf (Glu342-Lys686: for clarity the amino acid numbering of the full length

ovotransferrin is retained) was isolated and purified from hen egg white as reported earlier

(44). Guaranteed grade of chemicals, including pyrophosphoric acid from Wako Pure

Chemicals, NTA and Na2SO4 from Nacalai Tesque, were used for the kinetic and

crystallographic studies.

Kinetic experiments of Fe3+ release. The protein concentration of C-oTf was measured in

the apo form and iron bound holo form was prepared freshly in 100 mM Hepes, pH 7.4, using

Fe3+-NTA complex as the iron donor and large excess bicarbonate as the synergistic anion to

replace the bound NTA. The holo form was then equilibrated to 50 mM Mes, pH 5.6, by

dialysis and the bound iron was confirmed spectrophotometrically to retain at 1:1 molar ratio

with protein. Nitric acid-washed glassware and double distilled and de-ionized water were

used. Extreme care was taken to avoid any metal contamination and alteration of pH in all the

solutions. All the anion stock solutions were prepared freshly just before use in 50 mM Mes

and the pH was adjusted to 5.60 using NaOH.

The fast kinetics was measured using fluorescence mode of SX.18MV stopped-flow

reaction analyzer (Applied Photophysics Ltd. UK) as described in detail previously (43).

Measurement of complete iron release at pH 5.6 using different concentrations of anions

were, however, unsuccessful within the maximum time limit of the instrument (1000 s) due

to the slow rate iron release from C-oTf.

The complete iron removal was monitored using Hitachi F-3000 conventional fluorescence

spectrophotometer at (30±0.1)oC. The excitation and emission wavelengths were 285nm and

330nm, respectively. A protein concentration of 0.2 µM was used in all the experiments. The

kinetic experiments were always initiated by the addition of holo protein to a buffered

anion/chelator solutions and data points were collected every 10 s interval. The monophasic

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progress curves were best fit to a single exponential using Equation 1 either using built-in

software in the stopped-flow apparatus or by plotting the data points and analyzing using

KaleidaGraph (Synergy Software). In the single exponential equation:

Z(t)= 1-exp(- kobst) (Eq. 1)

Z(t) is the fraction of iron released (apo) form as detected by the change in fluorescence

emission intensity at time t, and kobs is the observed first-order rate constant. Minimum three

independent measurements for each anion concentration were done and average kobs values

were used for analysis.

Crystallization. The apo-form of C-oTf was crystallized using hanging-drop

vapor-diffusion method. The solution in the crystallization drop was prepared, on a silanized

coverslip, by mixing 5 µl of protein solution (25.0 mg/ml, pH 6.0, 0.05 M acetate buffer)

with 5 µl of precipitant solution (55% ammonium sulfate, pH 6.0, 0.05 M acetate buffer). The

droplets were equilibrated against 1 ml of the precipitant solution at 20 ºC. Crystals were

obtained within 1 month.

The apo crystals were subjected to diffraction experiments, using a Nonius precession

camera with Ni-filtered CuKα radiation generated by a Rigaku X-ray generator (40 kV, 20

mA). The precession photographs indicated that the apo crystal belongs to space group

P21212 with a cell dimension of a=103.58, b=81.13, c=50.08 Å (α=β=γ=90º).

Data collection and processing. Diffraction data were collected using CuKα radiation

(=1.5418 Å) with a Bruker Hi-star multiwire detector coupled to Mac Science M18XHF

rotating-anode generator. Total of 66,969 reflections were collected to 2.25 Å. The data were

processed, scaled and merged with Saint program (Bruker Analytical X-ray Instruments, Inc.,

Madison, WI). For multiple isomorphous replacement (MIR), crystals were soaked at 20 ºC

in the precipitant solution containing 0.2 mM p-chloromercuribenzene sulfonate, 2.0 mM

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K2PtCl4, 5.0 mM Sm2(SO4)3, 5.0 mM KAuCl4, 1.0 mM UO2(CH3COO)2, 10 mM AgNO3, or

5.0 mM methylmercury hydroxide. A number of heavy atom derivative data sets were

collected and processed in the same way. Only K2PtCl4, Sm2(SO4)3, and UO2(CH3COO)2

derivatives were, however, useable for MIR phasing. Details of the crystal parameter and

statistics of the data sets are given in Table 2. Three Pt, one Sm, and two U binding sites were

obtained with difference Patterson and difference Fourier method using program PHASES.

The obtained MIR phase was improved by solvent-flattening with PHASES. Statistics of the

phasing are shown in Table 2. Electron density map was made with the solvent flattened MIR

phase using the data between 15.0 and 3.5 Å. Domain 1 and domain 2 of the C-lobe of the

apo-ovotransferrin whole molecule (1AOV, 3.0 Å resolution) were translated and rotated to

fit the map, respectively, using TURBO-FRODO.

Structure refinement. The initial model made using MIR map and the structure of the

whole molecule of ovotransferrin was refined by simulated annealing with molecular

dynamics using a slow-cooling protocol implemented in X-PLOR (45) from 3000 to 300K.

This refinement yielded R = 0.228 for the data between 12.0 and 2.6 Å resolution. Several

rounds of restrained least squares refinement using CNS (46) up to the resolution of 2.3 Å,

followed by manual model building, were carried out to improve the model. One sulfate

anion and water molecules, and a carbohydrate moiety (N-acetyl glucosamine) having more

than 3 σ on the Fo-Fc map were then added to the model. The final model consisted of 341

amino acid residues, one sulfate anion, and 46 water molecules with a R value of 0.186

(Rfree=0.239) for 12,159 reflections with F>2σ(F) between 10.0-2.30 Å resolution (Table 2).

The electron density maps (2Fo-Fc, contoured at 1 σ) were calculated using the reflection

data at 10-2.3 Å resolution. The omit maps (Fo-Fc, contoured at 3 σ) were obtained from the

model in which a sulfate molecule was excluded.

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RESULTS

Anion-dependent Fe3+ release kinetics. To investigate functional characteristics of

ovotransferrin C-lobe, we did kinetic analyses for the anion-dependent Fe3+-release from

C-oTf. Initially, Fe3+-release kinetics was monitored using stopped-flow method and clear

monophasic progress curves were obtained at different concentrations of pyrophosphate,

sulfate, and NTA. Although none of the anions yielded complete iron removal in the time

span of 1000 s limited to the stopped-flow equipment, the data points, including the ones at

very early time after the stopped-flow mixing, were best fitted to the single exponential of

Equation 1. This was quite different from the Fe3+-release kinetics of the isolated N-lobe of

ovotransferrin, which displays a clear biphasic progress curves under the same conditions

(43). Monophasic progress curves have been also observed with the C-lobe monoferric

human serum transferrin (47).

For the quantitative analysis of the Fe3+-release kinetics, the complete iron removal time

course must be followed. The kinetic analysis of Fe3+-release was, therefore, done using a

conventional spectrofluorometer. Clear monophasic time course data were again obtained for

all the three anions during the complete iron removal within the reasonable time limit of

measurement (maximum 90 min) which is not affected by the instrumental drift. Figure 1

shows the apparent first-order rate constants obtained by the single exponential curve-fit of

the raw data to Equation 1 as a function of pyrophosphate concentration (panel A). Kinetic

measurements below 20 mM pyrophosphate concentration were unsuccessful because of

incomplete Fe3+ removal within the time span. The obtained kobs values showed an apparent

hyperbolic relation with increase in the pyrophosphate concentration.

The same analysis was done for the other two anions of different chemical nature. Sulfate,

which is a simple non-synergistic anion and NTA, a weak chelator anion that can also act as a

synergistic anion (48). In panels B and C of Figure 1 are shown the dependence of kobs values

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as functions of sulfate and NTA concentrations, respectively, and in both the cases they

appear to follow an hyperbolic pattern. NTA experiments above 100 mM were unsuccessful

due to large interference of NTA fluorescence with the one from protein under identical

experimental conditions.

Model presentation for the kinetic data. The simplest model that is consistent with a

non-linear (apparent hyperbolic) relation of the kobs value with anion concentrations (Fig. 1)

can be represented by Scheme 1:

K1 K3

X Y Z (Scheme 1)

K2

where ‘X’ represents the synergistic carbonate anion bound holo C-oTf and ‘Y’ represents an

additional anion (pyrophosphate, sulfate, or NTA) bound different conformer of ‘X’. The

reversible interconversion of ‘X’ and ‘Y’ are driven by apparent first-order rate constants K1

and K2 and Fe3+ release can occur only from ‘Y’ form with the apparent first-order rate

constant K3 leading to iron free apo form, ‘Z’. The constants K1, K2, and K3 correspond to the

true first-order rate constants or pseudo first-order rate constant, depending on their anion

concentration dependency. The fraction of apo-form (Z) at an Fe3+ releasing time t, can be

expressed by double-exponential equation as follows,

Z(t)= 1-{r2/(r2-r1) }exp(-r1t) + {r1/(r2-r1)}exp(-r2t) (Eq.2)

The apparent rate constants, r1 and r2 are related to the rate constants, K1, K2, and K3:

r1 = α - (α2- β)1/2 (Eq.3)

r2 = α + (α2- β)1/2 (Eq.4)

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2α= K1+K2+K3 (Eq.5)

β=K1K3 (Eq.6)

Equation 2 should give rise to a concave type of the biphasic Fe3+ release time course. The

apparent monophasic time courses, as observed, can be obtained when r2 is much higher than

r1. In this case (r2>>r1) , Equation 2 can be shown by the approximated form:

Z(t)= 1-exp(-r1t) (Eq.7)

Equation 7 yields the monophasic time course with the relation kobs= r1.

Since the Fe3+ release rate clearly depends on the anion concentration (Figure 1), and since

the anion binding as a crucial step for the Fe3+ release (49) has been widely believed, it was

examined by the curve-fitting analysis of the kobs data to Equation 7 whether the apparent

first-order rate constants (K1, K2, and K3) are true first-order rate constants or pseudo

first-order rate constants that correspond to the product of second-order rate constant and

anion concentration. When only K3 is the pseudo first-order rate constant, the curve-fitting of

kobs data to Equation 7 yielded a good fit for all the three anions but large errors were

obtained for both K2 and K3 values. The case of anion dependence of both K1 and K3 did not

yield any good curve-fitting. The best curve-fitting results were obtained when K1 is a pseudo

first-order rate constant but K2 and K3 are true first-order rate constants. The solid curves in

Figure 1 are the curve-fit lines for Equation 7 using the relation, K1=k1[A], where k1 and [A]

are a second-order rate constant and an anion concentration, respectively. For all the three

anions, the curve-fit lines apparently followed hyperbolic patterns within reasonably small

errors. The true kinetic constants obtained from this analysis are listed in Table 1. The

values were highest for pyrophosphate and lowest for NTA, depending on their

non-synergistic or synergistic nature, as also emphasized in the Fe3+ release mechanism in the

isolated N-lobe of ovotransferrin (43). This hierarchy for the kobs values has been also

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observed for the C-lobe monoferric human serum transferrin (37, 38, 47, 50).

Crystallographic Analysis of Apo C-oTf. To evaluate the single pathway kinetic model on

the structural basis, we did the X-ray crystallographic analysis for C-oTf that bound an anion

employed for the Fe3+ release kinetics. The apo form of C-oTf was crystallized in ammonium

sulfate solution and solved for the three dimensional structure by the isomorphous

replacement method. Relevant refinement statistics are given in Table 2. In the solved

structure, residues 342, 343, 420 and 424 are not included, because no clearly interpretable

electron density could be seen. The overall completeness, R-factor and free-R value were

63.6 %, 0.186 and 0.239, respectively, for the data more than 2σ (F). For the highest

resolution bin (2.30-2.38 Å), the completeness was 29.3 %, and the R-factor and free-R value

were, respectively, 0.243 and 0.296. From a Luzzati plot (51), the mean absolute error in

atomic position is estimated to be 0.26 Å.

A Ramachandran plot (52) of the main chain torsion angles shows that about 83.8% lie

within the core region, with 99.7% lying within the allowed region. One non-glycine residue

(Leu 636) lies outside the allowed regions of conformational space; it is in a γ-turn as in

corresponding Leu299 of the N-lobe.

Overall organization of the structure. Figure 2 (panel A) displays the overall structure of

apo ovotransferrin C-lobe as a Cα trace. The apo structure, when compared with the previous

holo (the Fe3+- and CO32--loaded form) C-lobe structure of the whole molecule of

ovotransferrin (16), comprises a domain-opened conformation. The mode and extent of the

opening were almost the same as in the C-lobe of the full-length molecule of ovotransferrin

(16, 27); as calculated by the rigid-body motion method (32), the domains move 36º around a

rotation axis passing through the two β-strands linking the domains.

One of the most important observations in Figure 2 (panel A) is that the binding of a

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single sulfate anion is clearly detected from an electron density map. It is located in the

interdomain cleft (sulfate 701) with reasonably low B-factors: the values are 42.9, 48.3, 44.4,

43.9, 41.0 Å2 for SO4701-S, -O1, -O2, -O3, and –O4, respectively.

Structure of Anion Binding Site. Figure 2 (panel B) displays the stereo diagram of the

electron density map (green/2Fo - Fc) for the sulfate anion located in the interdomain cleft.

The figure also shows the omit map (blue/Fo - Fc) calculated with the exclusion of sulfate

model. Sulfate 701 exists in close proximity to Thr 461 in a hinge strand and to

Fe3+-coordinating ligand residues of His 592 and Tyr 431. A water molecule (H2O 843) also

resides close to the sulfate anion.

Figure 3 shows the hydrogen bonding structures for the anion-binding site in C-oTf;

SO4-O3 forms a hydrogen bond with an Fe3+-coordinating ligand group His 592-NE2.

Another oxygen atom of the same sulfate anion (SO4-O2) makes a hydrogen bond with Thr

461-OG1 in helix 5 of the domain 2. A Fe3+-coordinating group Tyr 431-OH in an

interdomain hinge strand (16) resides very close to SO4-O2 (3.5 Å) and SO4-O4 (3.5 Å),

thereby probably forming weak hydrogen bonds. Another Fe3+-coordinating group Tyr

524-OH in domain 2 makes an indirect interaction with SO4-O1 and SO4-O4 through a water

molecule (H2O 843). The structural characteristics of the anion-binding site in C-oTf are

consistent with the view that the Fe3+-release from C-lobe largely depends on the anion

occupation of iron coordinating residue groups.

DISCUSSION

The data shown here is the first demonstration of the crystal structure and anion-dependent

Fe3+-release kinetics for isolated transferrin C-lobe. The present data for C-oTf, along with

the previous crystallographic (39) and kinetic (43) data for isolated ovotransferrin N-lobe,

provide crucial information for understanding the structural basis of some functional

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differences between the two lobes.

The Fe3+ binding properties are markedly different for the N and C lobes of transferrins,

although the two lobes assume very similar overall conformation. At acidic pH, the N lobes

of serum transferrin and ovotransferrin display less binding stability and more accelerated

release of Fe3+ than the C-lobe. The functional difference at acidic pH has been well

explained, on the basis of the structural (22, 24) and functional (40-42) evidence, by the

implications of the dilysine trigger mechanism in the N-lobe, but not in the C-lobe. An

alternative difference that the Fe3+ release from transferrins in presence of simple anions

(9-13) is much slower in the C-lobe than in the N-lobe (35-37), however, has been poorly

understood on the structural basis. The differential rate for the anion-mediated Fe3+ release

for the two lobes are observed in a wide range of pH, including neutral pH. The mode of

anion effects on the Fe3+ release kinetics is also different for the two lobes; a kinetically

significant anion binding (KISAB) proposed for the C-lobe is absent in the N-lobe (38). The

original model proposed by Bates and coworkers (49, 53) includes the binding of simple

anion to a different site from the synergistic carbonate anion binding site; this binding

induces the domain opening as the rate limiting step in the Fe3+ release pathway. Although

differential modes of the binding of simple anions with the two lobes of apo transferrins have

been demonstrated (54-56), no attempt has been made to directly compare the isolated N- and

C-lobes with respect to the anion-dependent Fe3+ release kinetics and the crystal structure of

the anion binding site.

According to our previous crystallographic data of the isolated N-lobe of ovotransferrin

(39), there are two SO42- binding sites (site 1 and site 2) in the interdomain cleft. Site 1

includes Ser 91-OG and His 250-NE2. The latter protein group is a consensus

Fe3+-coordinating ligand (15-24). Site 2 comprises Ser 122-N, Arg 121-NE, and Arg

121-NH2. The Arg groups are consensus CO32- anchor groups for holo transferrins (15-24). A

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protein group, Ser 122-N, forms a hydrogen bond in the holo structure (16) with an oxygen

atom (OD2) of Asp 60; the Asp residue is the only iron-coordinating ligand from domain 1

and plays a central role in the domain opening and closure (16). Taken together, the anion

binding to the N-lobe can be concluded to facilitate the Fe3+-release through multiple

mechanisms: the occupation of an iron ligand residue, the opening of the domains, and the

release of the synergistic carbonate anion. The structural characteristics of the anion binding

sites have been well-correlated with the kinetic mechanism for the anion-mediated Fe3+

release; the Fe3+ release from isolated ovotransferrin N-lobe follows a biphasic progress

curve and the results from quantitative kinetic analyses have been consistent with a

dual-pathway Fe3+ release mechanism (43).

Both the anion binding structure and Fe3+ release kinetics of C-oTf are markedly different

from those of ovotransferrin N-lobe; unlike the N-lobe, only one anion binding site exists in

the interdomain cleft (Figs. 2 and 3) and the Fe3+ release follows a simple monophasic

progress curve with much decelerated rate in C-oTf. The single bound SO42- in the

interdomain cleft of C-oTf interacts directly with Thr 461-OG1, Tyr 431-OH, and His

592-NE2, and indirectly with Tyr 524-OH through a H2O molecule (Fig. 3). The residue

groups, Tyr 431-OH, His 592-NE2, and Tyr 524-OH correspond to Fe3+-coordinating ligands.

The anion binding to the C-lobe is, therefore, considered to facilitate the Fe3+-release by the

occupation of the iron ligand residues. The C-lobe, however, lacks the synergistic anion

release and domain opening mechanisms, since there is no clear interaction of the sulfate

anion with the anchor residue Arg460 (the counterpart in C-lobe of Arg120) for synergistic

carbonate anion or with Thr461-N (the counterpart in C-lobe of Ser122-N) that receives a

hydrogen bond from the Fe3+-coordinating group Asp395-OD2 of the domain 1 in the holo

structure (16). This may be related to the slower rate of Fe3+ release from C-lobe than from

the N-lobe.

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In more details, the occurrence of the single anion binding site in the interdomain cleft in

C-oTf can be well related to the kinetic mechanism for the non-synergistic anion-mediated

Fe3+ release. The Fe3+ release from the C-lobe in presence of sulfate, pyrophosphate, or NTA

follows a monophasic single exponential time course. The apparent hyperbolic profiles of the

observed rate constant (kobs) values with anion concentration are analyzed consistent with a

single-pathway iron release model. In Figure 4 is shown a feasible structural mechanism

compatible with the crystal structures and with the two-step, single-pathway kinetic

mechanism of Fe3+ release from C-oTf (Scheme 1). The domain closed holo form ‘X’ in

which the synergistic carbonate anion and the side chains of Asp395, Tyr431, Tyr524, and

His592 make coordination to Fe3+ is transformed into putative CO32- and iron-loaded open

form ‘Y’ by non-synergistic anion (A) binding. The form ‘Y’ is still loaded with Fe3+ and

carbonate anion but newly binds a non-synergistic anion in the same anion binding sites as in

apo C-oTf (Figure 3); it corresponds to the ‘mixed-ligand’ intermediate, a quaternary

complex of (A· Trf· Fe3+· CO32-) with open-like structure similar to the one proposed by Bates

and coworkers (49, 53) for full-length transferrin. The structural states ‘X’ and ‘Y’

interconvert reversibly with a pseudo first order rate constant K1 (K1 = k1[A]) and with a true

first order rate constant K2. Because of the decreased interactions with the protein, Fe3+ along

with carbonate anion are released from the ‘mixed-ligand’ intermediate ‘Y’ with a first order

rate constant K3, yielding the anion bound apo form, ‘Z’; this process includes no further

addition of anion and is thus independent of anion concentration. This single pathway model

is kinetically supported by the curve fitting analysis (Fig. 1). Because of the differential Fe3+

release pathways, the obtained rate constants for the C lobe cannot be directly compared with

those for the N-lobe. When the second order rate constants for the rate-limiting,

domain-opening reactions (the constants k1 and k3 for the C- and N-lobes, respectively) are

compared for the two lobes, however, the value is 22 fold less in case of pyrophosphate for

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the C-lobe than for the N-lobe (Table 1 and reference 43). The apparent decelerated rate of

Fe3+ release from the C-lobe can be related, at least in part, to the decreased rate constant for

the domain opening.

In conclusion, the structural and functional differences between N- and C-lobes of

transferrins have been a major target in transferrin biochemistry. The present study of C-oTf

along with the previous N-lobe studies (39, 43) demonstrate that the difference in the anion

binding structures can be well correlated with the differential kinetic pathways of

anion-induced Fe3+ release in the two lobes. The absence in C-oTf of SO42- binding to the

synergistic anion binding groups Arg460-NE and –NH2 and to Thr461-N can be closely

related to the decelerated Fe3+ release in the C-lobe. It is, however, still not clear whether the

present SO42- binding site corresponds to the kinetically significant anion binding (KISAB)

site of the C-lobe (38). The KISAB site originally hypothesized for the C-lobe of human

serum transferrin as the binding site of a variety of simple anions (38) has been later

investigated by site-directed mutagenesis approach as the kinetically sensitive site toward

monovalent anion, Cl-; by this mutagenesis approach the residue Lys569 has been assigned

for the KISAB site (57). Unlike the sulfate anion (sulfate 701) binding site in C-oTf, the

residue Lys569 exists outside the interdomain cleft. For the conclusive localization of the

KISAB site, the chloride anion-bound crystal structure of transferrin C-lobe would be

necessary.

ACKNOWLEDGMENT

Computational time was provided by the Super-Computer Laboratory, Institute for Chemical

Research, Kyoto University.

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REFERENCES

1. Aisen, P., and Listowsky, I. (1980) Annu. Rev. Biochem. 49, 357-393

2. Thibodeau, S. N., Lee, D. C., and Palmiter, R. D. (1978) J. Biol. Chem. 253, 3771-3774

3. Mason, A. B, and Woodworth, R. C. (1984) J. Biol. Chem. 259, 1866-1873

4. Mason, A. B., Brown, S. A., and Church, W. R. (1987) J. Biol. Chem. 262, 9011-9015

5. Mason, A. B., Woodworth, R. C., Oliver, R. W. A., Green, B. N., Lin, L.-N., Brandts, J. F.,

Savage, K. J., Tam, B. M., and MacGillivray, R. T. A. (1996) Biochem. J. 319, 361-368

6. Arnold, R. R., Cole, M. F., and McGhee, J. R. (1977) Science 197, 263-265

7. He, J., and Furmanski, P. (1995) Nature 373, 721-724

8. Klausner, R. D., Ashwell, G., van Renswoude, J., Harford, J. B., and Bridges, K.R.

(1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2263-2266

9. Baldwin, D. A., and de Sousa, D. M. R. (1981) Biochem. Biophys. Res. Commun. 99,

1101-1107

10. Cheuk, M.S, Keung, W.M, and Loh, T.T. (1987) J. Inorg. Biochem. 30, 121-131.

11. Kretchmar, S.A., and Raymond, K.N. (1988) Inorg. Chem. 27, 1436-1441

12. Nguyen, S. A. K., Craig, A., and Raymond, K.N. (1993) J. Am. Chem. Soc. 115,

6758-6764

13. Bailey, C.T., Byrne, C., Chrispell, K., Molkenbur, C., Sakett, M., Reid, K.,

McCollum, K., Vibbard, D., and Catelli, R. (1997) Biochemistry 36, 10105-10108

14. Egan, T.J., Zak, O., and Aisen, P. (1993) Biochemistry 32, 8162-8167

15. Bailey, S., Evans, R. W., Garratt, R. C., Gorinsky, B., Hasnain, S., Horsburgh, C.,

Jhoti, H., Lindley, P. F., Mydin, A., Sarra, R., and Watson, J. L. (1988) Biochemistry 27,

5804-5812

16. Kurokawa, H., Mikami, B., and Hirose, M. (1995) J. Mol. Biol. 254, 196-207

17. Haridas, M., Anderson, B. F., and Baker, E. N. (1995) Acta Cryst. D 51, 629-646

by guest on October 1, 2017

http://ww

w.jbc.org/

Dow

nloaded from

20

18. Rawas, A., Muirhead, H., and Williams, J. (1996) Acta Cryst. D 52, 631-640

19. Moore, S. A., Anderson, B. F., Groom, G. R., Haridas, M., and Baker, E. N. (1997)

J. Mol. Biol. 274, 222-236

20. Sharma, A. K., Paramasivam, M., Srinivasan, A., Yadav, M. P., and Singh, T. P. (1999)

J. Mol. Biol. 289, 303-317

21. Sarra, R., Garratt, R., Gorinsky, B., Jhoti, H., and Lindley, P. (1990) Acta Cryst. B 46,

763-771

22. Dewan, J. C., Mikami, B., Hirose, M., and Sacchettini, J.C. (1993) Biochemistry 32,

11963-11968

23. Day, C. L., Anderson, B.F., Tweedie, J.W., and Baker, E. N. (1993) J. Mol. Biol. 232,

1084-1100

24. MacGillivray, R. T. A., Moore, S. A., Chen, J., Anderson, B. F. Baker, H., Luo, Y.,

Bewley, M., Smith, C. A., Murphy, M. E. P., Wang, Y., Mason, A. B., Woodworth, R. C.,

Brayer, G. D., and Baker, E. N. (1998) Biochemistry 37, 7919-7928

25. Rawas, A., Muirhead, H., and Williams, J. (1997) Acta Cryst. D 53, 464-468

26. Jeffrey, P. D., Bewley, M. C., MacGillivray, T. A., Mason, A. B., Woodworth, R. C., and

Baker, E. N. (1998) Biochemistry 37, 13978-13986

27. Kurokawa, H., Dewan, J. C., Mikami, B., Sacchettini, J. C., and Hirose, M. (1999)

J. Biol. Chem. 274, 28445-28452

28. Grossmann, J. G., Neu, M., Pantos, E., Schwab, F. J., Evans, R. W., Townes-Andrews,

E., Lindley, P. F., Appel, H., Thies, W. -G., and Hasnain, S. S. (1992) J. Mol. Biol. 225,

811-819

29. Grossmann, J. G., Neu, M., Evans, R. W., Lindley, P. F., Appel, H., and Hasnain, S. S.

(1993) J. Mol. Biol. 229, 585-590

30. Mecklenburg, S. L., Donohoe, R. J., and Olah, G. A. (1997) J. Mol. Biol. 270, 739-750

by guest on October 1, 2017

http://ww

w.jbc.org/

Dow

nloaded from

21

31. Grossmann, J. G., Crawley, J. B., Strange, R. W., Patel, K. J., Murphy, L. M., Neu, M.,

Evans, R. W., and Hasnain, S. S. (1998) J. Mol. Biol. 279, 461-472

32. Gerstein, M., Anderson, B. F., Norris, G. E., Baker, E. N., Lesk, A. M., and Chothia, C.

(1993) J. Mol. Biol. 234, 357-372

33. Mizutani, K., Mikami, B., and Hirose, M. (2001) J. Mol. Biol. 309, 937-947

34. Gerstein, M., Lesk, A. M. & Chothia, C. (1994). Biochemistry, 33, 6739-6749

35. Kretchmar, S.A., and Raymond, K.N. (1986) J. Am. Chem. Soc. 108, 6212-6218

36. Bali, P.K., and Harris, W.R. (1989) J. Am. Chem. Soc. 111, 4457-4461

37. Bali, P.K., Harris, W.R., and Nosset-Tollefson, D. (1991) Inorg. Chem. 30, 502-508.

38. Egan, T.J., Ross, D., Purves, L.R., and Adams, P.A. (1992) Inorg. Chem. 31, 1994-1998

39. Mizutani, K., Yamashita, H., Mikami, B., and Hirose, M. (2000) Biochemistry 39,

3258-3265

40. Steinlein, L.M., Ligman, C.M., Kessler, S., and Ikeda, R.A. (1998) Biochemistry 37,

13696-13703

41. Li, Y., Harris, W.R., Maxwell, A., MacGillivray, R.T.A., and Brown, T. (1998)

Biochemistry 37, 14157-14166

42. He, Q-Y., Mason, A.B., Tam, B.M., MacGillivray, R.T.A., and Woodworth, R.C. (1999)

Biochemistry 38, 9704-9711

43. Muralidhara, B.K. and Hirose, M. (2000) J. Biol. Chem. 275, 12463-12469

44. Oe, H., Doi, E., and Hirose, M. (1988) J. Biochem. 103, 1066-1072

45. Brünger, A. T., Karplus, M. & Petsko, G. A. (1989). Acta Crystallog. sect. A 45, 50-61

46. Brünger, A. T., Adams P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve,

R. W., Jiang, J., Kuszewski, J., Nilges, M., Pannnu, N. S., Read, R. J., Rice, L. M.,

Simonson, T., and Warren, G. L. (1998) Acta Crystallog. sect. D 54, 905-921

47. Marques, H.M., Walton, T., Egan, T.J. (1995) J. Inorg. Biochem. 57, 11-21

by guest on October 1, 2017

http://ww

w.jbc.org/

Dow

nloaded from

22

48. Schlabach, M.R., and Bates, G.W. (1975) J. Biol. Chem. 250, 2182-2188

49. Cowart, R.E., Swope, S., Loh, T.T., Chasteen, N.D., and Bates, G.W. (1986)

J. Biol. Chem. 281, 4607-4614

50. Li, Y., and Harris, W.R. (1998) Biochim. Biophys. Acta 1387, 89-102

51. Luzzati, V. (1952) Acta Crtstallog. 5, 802-810

52. Ramakrishnan, C., and Ramachandran, G. N. (1965) Biophys. J. 5, 909-933

53. Cowart, R.E., Kojima, N., and Bates, G.W. (1982) J. Biol. Chem. 257, 7560-7565

54. Oe, H., Takahashi, N., Doi, E., and Hirose, M. (1989) J. Biochem. 106, 858-863

55. Harris, W.R., and Cafferty, A.M., Trankler, K., Maxwell, A., MacGillivray, R.T.A.

(1999) Biochim. Biophys. Acta 1430, 267-280

56. Cheng, Y., Mason, A., and Woodworth, R.C. (1995) Biochemistry 34, 14879-14884

57. Zak, O., Tam, B., MacGillivray, R.T.A., Aisen, P. (1997) Biochemistry 36, 11036-11043

58. Kraulis, P. J. (1991) J. Appl. Cryst. 24, 946-950

59. Merritt, E. A., and Bacon, D.J. (1997) Meth. Enz. 277, 505-524

by guest on October 1, 2017

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FOOTNOTES

1 The abbreviations used are: C-oTf, isolated C-lobe (C-terminal half-molecule) of

ovotransferrin; NTA, nitrilotriacetate.

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(FIGURE LEGENDS)

Fig. 1. Anion concentration dependence of the apparent first-order rate constants for

Fe3+ release. The observed rate constant kobs values obtained from curve-fit of the raw data

to Equation 1 in the text are shown as a function of (A) pyrophosphate, (B) sulfate, and (C)

NTA concentrations. The best fit of the kobs values to Equation 7 in the text is represented by

the solid line and the corresponding correlation coefficient (R) is also shown in each plot.

Fig. 2. Stereo views depicting Cαα traces of C-oTf (A) and electron density map of the

sulfate anion binding site (B). In A, the apo and holo forms of ovotransferrin C-lobe are

shown in purple and cyan, respectively. The figures are produced with MOLSCRIPT (58)

and Raster3D (59) as the superimposed ones on domain N2. The holo structure is drawn

using the previous data (PDB, 1OVT) (16). The residue numbers are labeled for the apo form.

The sulfur and oxygen atoms of bound sulfate anions are shown by yellow and orange

spheres, respectively. In B, the electron density map (green: 2Fo - Fc, contoured at 1σ) was

calculated for the sulfate 701 binding site. The omit map (blue: Fo - Fc, contoured at 3σ) was

obtained from the model in which the sulfate molecule was omitted. The final model is

superimposed in stick presentation with atoms in standard colors.

Fig. 3. Diagram of the hydrogen bonding network around the sulfate 701 binding site in

the interdomain cleft. The residues of C-oTf are numbered on the full length molecule of

ovotransferrin and the residues in parenthesis represent the corresponding residues in the

N-lobe. The dotted lines display atom to atom interactions with the bond distances in Å; they

are all hydrogen bond interactions, although the hydrogen bonds of Tyr431-OH to SO4-O2

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and SO4-O4 and of Tyr524-OH to H2O may be weak ones.

Fig. 4. Feasible structural model for the single-pathway kinetics of Fe3+ release from

C-oTf. The Fe3+ coordinations are shown by the arrows and the hydrogen bonds, by dotted

lines. The structural transformations from ‘X’ to ‘Y’ and from ‘Y’ to ‘X’ occur with the

respective rate constants of k1[A] and K2 and the Fe3+ release from ‘Y’ to ‘Z’ proceeds with

K3, where k1 is the second-order rate constant and K2 and K3 are first-order rate constant. ‘A’

represents anion and other details are described in the text.

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TABLE 1 Rate constants included in the Fe3+ release pathway from C-oTf

The rate constants were obtained by the curve-fitting analyses using Equation 7 (see

Figure 1), on the basis of the Fe3+ release pathway defined as Scheme 1 in the text. The

constants K2 and K3 are the true first order rate constants, but the constant K1 is a pseudo-first

order rate constant with the relation of K1=k1[A], where k1 and [A] are the second order rate

constant and an anion concentration, respectively.

Rate constants Anion

k1 (min-1M-1) K2 (min-1) K3(min-1)

Pyrophosphate 8.67 ± 4.49 1.24 ± 0.49 1.01 ± 0.19

Sulfate 5.67 ± 3.30 0.91 ± 0.21 0.55 ± 0.08

NTA 2.01 ± 1.58 0.06 ± 0.03 0.13 ± 0.04

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TABLE 2 Summary of data collection and refinement Native K2PtCl4 Sm2(SO4)3 UO2(CH3COO)2 A. Crystal data Space group P21212 P21212 P21212 P21212 Cell dimensions a (Å) 103.58 103.76 104.50 104.53 b (Å) 81.13 81.53 82.10 82.34 c (Å) 50.08 50.26 50.29 50.62 Vm (Å3/Da) 2.6 Molecules per asymmetric unit 1 Observed reflectios 66,969 45,541 20,479 57,843 Resolution (Å) 2.25 2.64 3.13 2.70 Independent reflections 14,495 11,904 7,197 11,972 completeness (%) 70.1 90.7 88.9 94.7 Rsym (%) 5.8 8.5 5.8 21.9 Soak concentration (mM) 2.0 5.0 1.0 time (hr) 2 1 48 Phasing ( ∞ -3.5 Å) Rculis (centric) 0.601 0.606 0.602 Rkraut (acentric) 0.207 0.095 0.110 Number of heavy atoms 3 1 2 Phasing power 0.95 1.36 1.68 Figure of merit 0.517 Figure of merit after solvent flattening 0.795 B. Refinement statistics Resolution limits (Å) 10.0-2.30 No. of reflections used (F > 2σ(F)) 12,159 completeness (%) 63.6 No. of protein atoms 2,647 No. of solvent molecules 46 Ions 1SO4

2- Final R-factor 0.186 Free R value 0.239 Average B-factor (Å2) 42.2 r.m.s. deviation from ideal geometry Bond distances (Å) 0.0051 Bond angles (deg.) 1.23 Dihedrals (deg.) 22.1 Improper dihedrals (deg.) 0.725 C. Conditions for crystallization Concentration of the protein (mg/ml) 25.0 Buffer 50 mM Acetate pH 6.0 Precipitant 55 % Ammonium sulfate Salt 0.2 M MgCl2 “Native” is the apo crystal without the soaking with a metal ion. “K2PtCl4”, “Sm2(SO4)3”, and “UO2(CH3COO)2 ” reperesent the crystals soaked with K2PtCl4, Sm2(SO4)3, and UO2(CH3COO)2 , respectively. Phasing parameters were calculated at ∞ -3.5 Å resolution.

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and Masaaki HiroseKimihiko Mizutani, BK Muralidhara, Honami Yamashita, Satoshi Tabata, Bunzo Mikami

binding site and its implications for the kinetic pathway2-identified SO4 release mechanism in ovotransferrin C-lobe: A structurally3+Anion-mediated Fe

published online July 20, 2001J. Biol. Chem. 

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