Nucleotide metabolism

University of Veterinary Medicine

Department of Physiology and Biochemistry

DNA is stored in the nucleus of

eucaryotes, RNA found in cytoplasm or

ribosomes

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Structure of

nucleic acids

Structure of nucleotides and nucleosides

• Nucleotide = base + pentose + phosphate

N-glycosidic bond

(Phosphate) ester

bond

Nucleoside =

base + pentose

Pentose: ribose or

(2-)deoxy-ribose

• Nucleotide = base + pentose + phosphate

• Bases:

– Purine bases

purine

adenine

(6-amino-purine)

guanine

(2-amino-

6-oxo-purine)

Structure of purine nucleotides

(purine bases)

Bound to ribose (RNA)

or deoxyribose (DNA)

• Nucleotide = base + pentose + phosphate

• Bases:

– Pyrimidine bases pyrimidine

cytosine

(2-oxo-

4-amino-pyrimidine)

uracil

(2,4-dioxo-pyrimidine)

Keto-enol

tautomery(example: uracil)

thymine

(5-methyl-

uracil)

Structure of pyrimidine nucleotides

(pyrimidine bases)

Structure of nucleotides• Uracil: bound only to ribose

• Thymine: bound only to deoxyribose

• Cytosine: bound to ribose or deoxyribose

Purine nucleosides:

(deoxy)adenosine, (deoxy)guanosine

Pyrimidine nucleosides:

uridine, (deoxy)cytidine, deoxythymidine

Nucleotides:

nucleoside + mono-/di-/triphosphate:

(d-)adenylic acid, (d-)guanylic acid, uridylic

acid, (d-)cytidylic acid, d-thymidylic acid

Synthesis of purine nucleotides (de novo)

glucose glucose 6-

phosphate

hexokinase

ATP ADP

ribose 5-phosphatepentose phosphate

pathway

PRPP

synthetase

ATP

AMP

5-phosphoribosyl-1-pyrophosphate (PRPP)

5-phosphoribosyl-amine

PRPP amidotransferase*glutamine

glutamate

P – P

5-phosphoribosyl-amine

glycine

N10-formyl-FH4 (FH4=tetrahydro folic acid)

FH4

glutamine

glutamate

HCO3-

H2O

aspartate

fumarate

N10-formyl-FH4

FH4

inosine monophosphate (IMP)

HCO3-

Asp

formyl

Gly

formyl

Gln

phosphoribosyl-amine

inosine monophosphate (IMP)

xanthosine monophosphate

IMP

dehydrogenase H2O

NAD+

NADH+H+

adenylosuccinate synthetase

adenylosuccinate

aspartate

GTP GDP

+Pan

glutamine

glutamate

ATP

AMP + PPGMP synthetase fumarate

guanosine monophosphate (GMP)

adenosine monophosphate (AMP)

adenylosuccinate

lyase

ribose

ribose

ribose

ribose

ribose

guanosine monophosphate (GMP) adenosine monophosphate (AMP)

ATP

ADP

ATP

ADP

nucleotide kinase nucleotide kinase

guanosine diphosphate (GDP) adenosine diphosphate (ADP)

nucleoside

diphosphate kinase

ATP

ADP

guanosine triphosphate (GTP)

Pin

oxidative

phosphorylation

substrate level

phosphorylation

adenosine triphosphate (ATP)

• Allosteric regulation:

– „+” effector: PRPP

– „-” effector: IMP, GMP, AMP

• Localization: each cell type, cytosol

• Needs lots of energy! (8 ATP)

PRPP amidotransferase*

AMPnucleotidase

Pin

adenosine

adenine

Pin

ribose-1-P

nucleoside

phosphorylase

H2O

NH3

adenine

deaminase

hypoxanthine

Degradation of purine nucleotides

AMP

Hypoxanthine

hypoxanthine

H2O

FAD

FADH2

xanthine oxidase

xanthine

H2O

FAD

FADH2

xanthine oxidase

uric acid

CO2

uricase

allantoine

Excreted by the

urine in primates,

birds and reptiles

Excreted by the urine in other species

(dog, cat, horse, ruminants, pig etc.)

Exception: dalmatian dog!

2H2O+O2

H2O2

GMPnucleotidase

Pin

guanosine

guanine

Pin

ribose-1-P

nucleoside

phosphorylase

H2O

NH3

guanine

desaminase

xanthine

uric acid

allantoine

guanine

GMP

xanthine

• Localization: each cell type, cytosol

– Only until uric acid!

• Uric acid → allantoine reaction only in the liver

– Allantoine is excreted by the urine

• Clinical relevance:

– Uric acid is very bad soluble in water precipitation in

joints, serosal membranes, kidneys inflammation

gout / uricosis

– Treatment: allopurinol

• Similar structure to hypoxanthine competitive

inhibition of xanthine oxidase

Uricosis: precipitated uric acid crystals in the kidney of a snake

Photo by Dr. János Gál

Gout in human

Visceral gout in poultry

Gout in parrot

Uricosis:

tophus-formation (H.E.)

Urate crystals

Proliferating cells

Urate kidney stones of Dalmatian dog

• Transport of uric acid happens by 2 different

transport processes in the liver:

• 80% fast Transport

20% slow Transport

• Dalmatian: fast transport gene of uric acid in the

liver has been mutated uricase is active in the

liver, but no uric acid uptake Excretion: mostly

uric acid, but also some allantoine uric acid

can be precipitated in the joints (gout) or kidney

(kidney stones).

Urolithiasis in dalmatian dog: urate crystals in the urine sediment

Urolithiasis in dalmatian dog: ectomised stones after surgery

• Nucleotide = base + pentose + phosphate

• Bases:

– Pyrimidine bases pyrimidine

cytosine

(2-oxo-

4-amino-pyrimidine)

uracil

(2,4-dioxo-pyrimidine)

Keto-enol

tautomery(example: uracil)

thymine

(5-methyl-

uracil)

Revision: structure of nucleotides

HCO3-

carbamoyl

phosphate

synthetase II.

glutamineglutamate

2 ATP2 ADP +Pin

carbamoyl-P aspartate

aspartate

transcarbamoylase

N-carbamoyl

aspartate

*

dihydroorotase

dihydroorotate

*

Synthesis of pyrimidine nucleotides

(de novo)

Pin

H2O

dihydroorotate

NAD+

NADH+H+

dihydroorotate

dehydrogenase

orotateorotate phosphoribosyl

transferase

PRPP

P-P

orotidylateorotidylate decarboxylase

CO2

uridine monophosphate

(UMP)

dihydroorotate

NAD+

NADH+H+

dihydroorotate

dehydrogenase

orotateorotate phosphoribosyl

transferase

PRPP

P-Pin

orotidylateorotidylate decarboxylase

CO2

uridine monophosphate

(UMP)

UMP kinase

ATP ADP

UDP

nucleoside

diphosphate

kinase

ADP

ATP

UTP

CTP synthetase

ADP +Pan

ATP

glutamate

glutamine

cytidinetriphosphat

(CTP)

*

• Localization: each cell type, cytosol

• Regulation:

Carbamoylphosphate synthetase II. (eukaryotes)– Positive allosteric effector: PRPP

– Negative allosteric effector: UTP

Aspartate transcarbamoylase (prokaryotes)

CTP-synthetase– Positive (+)allosteric effector: GTP

– Negative (-)allosteric effector: CTP

• Needs lots of energy! (7 ATP)

*

*

*

Localization and regulation

CMPCMP-deaminase

H2O NH3

UMPnucleotidase

Pin

uridine

Nucleoside

phosphorylase

Pan ribose-1-P

uracil

NADH+H+

NAD+

Pyrimidine dehydrogenase

dihydro-uracil

H2O

ureido-propionateureido-

propionase

NH3CO2

β-alanine

CO2

NH3

acetate

- Localization: each cell type, cytosol

- Regulation: depends on the amount of

nucleotides to be degradated

HS-CoA

dihydro-

pyrimidinase

Degradation of pyrimidine nucleotides

Resynthesis of nucleotides (salvage pathway)

Each nucleotide: nucleoside

ATP ADP

nucleoside kinasenucleotide

Purin nucleotides:adenine

PRPP PPin

Adenine-

phosphoribosyltransferaseAMP

guanine

hypoxanthine

guanine

xanthine

GMP

IMP

GMP

XMP

PRPP PPin

PRPP PPin

hypoxanthine-guanine-

phosphoribosyltransferase

(HGPRT)

xanthine-guanine-

phosphoribosyltransferase

(XGPRT)

eukaryotes:

prokaryotes:

Synthesis of deoxyribonucleotides

ADP

GDP

CDP

UDP

dADP

dGDP

dCDP

dUDP

ribonucleoside-diphosphate-reductaseH2O

FAD FADH2

thioredoxin-redctase

NADPH+H+ NADP+

Instead of

thioredoxin

could be

glutathione

also!

ATP ADP

dATP

dGTP

dCTP

dUTP

dUTPase/ dUTP-

phosphataseP-Pan

dUMP

dTMP

thymidilate synthase

N5,N10-methylene-

FH4

FH2

ATP

ADP

dTDP

ADP ATP

dTTP

nucleoside

diphoshosphate

kinase

Ascorbic aciddehydroascorbic

acid

Cobalamin is

needed also!

thioredoxin thioredoxin

Degradation of deoxyribonucleotides

• Differences compared to the degradation of ribonucleotides:– Nucleoside phosphorylase releases deoxy-ribose-1-

P from deoxyribonucleosides

– At purine bases: no differences in steps of degradation

– At pyrimidine bases: differences in steps of degradation are as follows:

• Deoxythymidine has one more methyl group, that s why instead of ureidopropionate ureidoisobutyrate will be produced. The endproduct is instead of β-alanine β-amino-isobutyrate

• Localization: in each cell type, cytosol