Metabolism ofnucleotides

Tomáš Kučeratomas.kucera@lfmotol.cuni.cz

Department of Medical Chemistry and Clinical Biochemistry2nd Faculty of Medicine, Charles University in Prague andMotol University

Hospital

MMXVIII

Nucleotides

P P P O

HOH

H

(O)H

H

N

H

O

–het e

r o c y cle–

N

nucleotide(nucleoside triphosphate)

nucleobasethe term established historicallynitrogen containing heterocyclic compounds

pyrimidinepurinenicotinamide, flavine, DMB…

Pyrimidine bases and nucleosides

N1C2N3

C4C5

C6

glutamine amideaspartate

HCO–3

NH

O

NH

O

uracil (Ura)

NH

O

N

NH2

cytosine (Cyt)

NH

O

NH

O

CH3

thymine (Thy)

N

OHOH

OH

O O

NH

O

uridine (U)

N

OHOH

OH

O O

N

NH2

cytidine (C)

N

OH

OH

O O

NH

O

CH3

deoxythymidine (dT)

Purine bases and nucleosides

N1

C2

N3 C4 N

H

9C8

N7C5

C6

glutamine amide

aspartate

amine

HCO–3

formateformate

glycine

N NH

N

NH2

N

adenine (Ade)

H2N N NH

N

O

NH

guanine (Gua)

N NH

N

O

NH

hypoxanthine (Hyp)

O N NH

N

O

NH

xanthine (Xan)

N N

OHOH

OH

O

N

NH2

N

adenosine (A)

H2N N N

OHOH

OH

O

N

O

NH

guanosine (G)

N N

OHOH

OH

O

N

O

NH

inosine (I)

O N N

OHOH

OH

O

N

O

NH

xanthosine (X)

“Unusual” bases and nucleosides

NH

O

N

NH2

CH3

5-methylcytosine (m5Cyt, mCyt)

NH

O

N

NH2

CH2OH

5-hydroxymethylcytosine (hm5Cyt, hmCyt)

O

OHOH

OH

O

NH

O

NH

pseudouridine (Ψ)

NH

O

N

NH2O

5-formylcytosine (f5Cyt)

NH

O

N

NH

CH3

N-4-methylcytosine (m4Cyt)

N NH

N

NH

N

N-6-methyladenine (m6Ade, mAde)

“Unusual” bases and nucleosides

Ang

ew.C

hem.Int.E

d.51,7110–7131,

2012

Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12

Xanthine alcaloids

O N

CH3

N

N

CH3O

NCH3

caffeine

O N

CH3

N

N

CH3O

NH

theobromine

O N

CH3

N

NH

O

NCH3

theophylline

Function of nucleotides

precursors (andmonomeric units) of DNA and RNAATP, GTP, CTP, UTP, dATP, dGTP, dCTP, dTTP

components of enzyme cofactorsNAD(P), FAD, FMN, CoA, cobalamin, [P]APS

macroergic “energy quanta” carriersATP, GTP

activated intermediates in biosynthesesUDP-sugars, CDP-diacylglycerols, S-adenosylmethionine

“secondmessengers” in signal transductioncAMP, cGMP

allosteric regulatorsATP, ADP, AMP

Gaining nucleotidespancreatic (deoxy)ribonucleases and intestinalpolynucleotidases: NA nucleotidesnucleotidase of epithelial cells of the intestine:

nucleotides nucleosidesin the intestinal epithelial cells, nucleosides are

used intact[hydro/phosphoro]lyzed bynucleosid[ases/phosphorylases]:

nucleoside + [H2O/ P ]base + pentose[-1-phosphate]

— salvage for the cell’s own need— transport to the blood

about 5% of ingested nucleotides into the blood asbases and nucleosideslow dietary uptake⇒ need of biosynthesis (recycling)biosynthesis energetically demanding⇒ recyclingadvantageous

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Biosynthesis of pyrimidine nucleosides – UTP,CTP

UTP synthesisUMP + ATP

nucleosidemonophosphate

kinase UDP + ADP

UDP + ATPnucleosidediphosphate

kinase UTP + ADP

CTP synthesis

N

OHOH

OPPP

O O

NH

O

UTP

glutamine glutamate

ATP+H2O ADP+ P

CTP synthetaseN

OHOH

OPPP

O O

N

NH2

CTP

Regulation of pyrimidine nucleotides synthesis

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

carbamoylphosphate synthetase IIactivation by ATP, PRPPinhibition by UDP, UTP

OMP-decarboxylasecompetitive inhibition by UMP (alittle also CMP)

Salvage pathways of pyrimidine nucleotides

Formation of nucleosidesUra(Cyt) + d-ribose-1-phosphate

pyrimidinenucleoside

phosphorylase U(C) + P

Thy + d-deoxyribose-1-phosphatethymidinephosphorylase

dT + P

Formation of nucleotidesU(C) + ATP

uridine-cytidine

kinase UMP(CMP) + ADP

dT + ATPdeoxythymidine

kinase dTMP + ADP

dC + ATPdeoxycytidine

kinase dCMP + ADP

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 2

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 3

Formation of NTPspecific nucleosidemonophosphate kinases

no deoxyribose-ribose discrimination

AMP + ATPadenylate

kinase ADP + ADP

GMP + ATPguanylate

kinase GDP + ADP

non-specific nucleoside diphosphate kinasesnon-specific to both substrates and also to NDP (NTP) anddNDP (dNTP)

GDP + ATPnucleosidediphosphate

kinase GTP + ADP

Regulation of purine nucleotides synthesis

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

ribose phosphatepyrophosphokinase(PRPP-synthetase)

inhibition by ADP, GDP

amidophosphoribosyltransferase

activation by PRPPinhibition by all A and Gnucleotides, XMP

adenylosuccinate synthetaseinhibition by AMPpowered by GTP

IMP-dehydrogenaseinhibition by GMP

GMP-synthetasepowered by ATP

Salvage pathways of purine nucleotides

purines biosynthesis in the liver, brain, neutrophiles…nucleosides and free bases transported to other tissuesfor example lymphocytes use the salvage pathways asthe main nucleotides source

Salvage pathways of purine nucleotides

FREE BASES

adenine APRT

PRPP P – P

AMP 5′-nucleotidase

P

adenosine

NUCLEOTIDES NUCLEOSIDES

NH3

AMPdeaminase

IMPP – PPRPP

HGPRThypoxanthin 5′-nucleotidase

P

inosin

GMPP – PPRPP

HGPRTguanin 5′-nucleotidase

P

guanosin

adenosinedeaminase

NH3

Pribose-1-phosphate purine nucleoside phosphorylase

Pribose-1-phosphate

purine nucleoside phosphorylase

ATPADP

adenosine kinase

Lesch-Nyhan syndrome

uric acid overproductiongout symptomesneurological abnormalities, mental retardation,agressivity, self-mutilation

deficiency of HGPRT (X chromosome)⇓

amidophosphoribosyltransferase activation⇓

overproduction and increased degradation of purinenucleotides

Purine-nucleotides cycle

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

combines biosynthetic and salvage enzymes of purinenucleotides metabolismanaplerotic pathway of the citrate cycle in skeletalmuscles

Formation of deoxyribonucleotides

Smith,

C.,Marks,A

.D.,Lieb

erman

,M.:Marks’b

asicmed

icalbioc

hemistry:

aclinicalap

proa

ch,Lippinc

ottW

illiams&

Wilk

ins,20

04(2nd

edition)

reduction at the NDPphosphorylation levelribonucleotide reductase

+ Fe3+, O2–

radical mechanism2 allosteric sites

activityspecificity

Substrate Effector ofactivity specificity

no dATP NDPCDP ATP ATP or dATPUDP ATP ATP or dATPGDP ATP dTTPADP ATP dGTP

Deoxythymidine synthesis

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

dUTP + H2O dUMP + P PdUDP + H2O dUMP + PdCMP + H2O dUMP + NH3

← thymidylate synthase

dTMP + ATP dTDP + ADPdTDP + ATP dTTP + ADP

prevention of dU in DNA

Degradation of purine nucleotides

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Degradation of uric acid

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Humans do not degrade it⇒ goutelevated levels of uric acid in bodyfluidsdeposition in various tissues (joints,kidneys...)

deficient excretionLesch-Nyhan syndromedeficiency of glucose-6-phosphatase

allopurinol

Degradation of pyrimidine nucleotides

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Synthesis of NAD(P)

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Synthesis of flavine “nucleotides”

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

The End

konec – the end

Thank you for your attention!

Pyrimidine bases and nucleosides

N1C2N3

C4C5

C6

glutamine amideaspartate

HCO–3

NH

O

NH

O

uracil (Ura)

NH

O

N

NH2

cytosine (Cyt)

NH

O

NH

O

CH3

thymine (Thy)

N

OHOH

OH

O O

NH

O

uridine (U)

N

OHOH

OH

O O

N

NH2

cytidine (C)

N

OH

OH

O O

NH

O

CH3

deoxythymidine (dT)

Purine bases and nucleosides

N1

C2

N3 C4 N

H

9C8

N7C5

C6

glutamine amide

aspartate

amine

HCO–3

formateformate

glycine

N NH

N

NH2

N

adenine (Ade)

H2N N NH

N

O

NH

guanine (Gua)

N NH

N

O

NH

hypoxanthine (Hyp)

O N NH

N

O

NH

xanthine (Xan)

N N

OHOH

OH

O

N

NH2

N

adenosine (A)

H2N N N

OHOH

OH

O

N

O

NH

guanosine (G)

N N

OHOH

OH

O

N

O

NH

inosine (I)

O N N

OHOH

OH

O

N

O

NH

xanthosine (X)

“Unusual” bases and nucleosides

Ang

ew.C

hem.Int.E

d.51,7110–7131,

2012

Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12

“Unusual” bases and nucleosides

Ang

ew.C

hem.Int.E

d.51,7110–7131,

2012

Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12

“Unusual” bases and nucleosides

Ang

ew.C

hem.Int.E

d.51,7110–7131,

2012

Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12

“Unusual” bases and nucleosides

Ang

ew.C

hem.Int.E

d.51,7110–7131,

2012

Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12Ang

ew.C

hem.Int.E

d.51,7110–7131,20

12

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Biosynthesis of pyrimidine nucleosides – UMP

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Purine nucleotides biosynthesis 1

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Synthesis of NAD(P)

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Synthesis of NAD(P)

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Synthesis of flavine “nucleotides”

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Synthesis of flavine “nucleotides”

Voet,D

.,Vo

et,J.G

.:Bioc

hemistry,John

Wile

y&So

ns,Inc

.,20

11(4th

edition)

Deoxythymidine synthesis