nucleotide biosynthesis

1NUCLEOTIDE BIOSYNTHESIS

Functions of Nucleotides Are Diverse

1.

2.

3.

6.

5.

4.

in carbohydrate, lipid, protein, and nucleic acid synthesis

Nucleotide Assembly

O

C

C C

C

OHOH

PPP

N

N

ribose nt biosynthesisNADPH reduction rxns

carbon skeleton

(source of carbons)

H (NADPH)

(nitrogen source)

CH2(N2)

2Nucleotide Synthesis

activated ribose (PRPP) + baseactivated ribose (PRPP) + ATP + amino acids (CO2 + N2)

sugar ring is activated at the

O

C

C C

C

OHOH

P CH2

HH H

H

OH

ribose-5-PO45-phospho-ribosyl-1-pyrophosphate

-configurationO

C

C C

C

OHOH

P CH2

HH H

H

OP

P

Activation of the Ribose Sugar for Nt Biosynthesis

2nd step

1st step

O

C

C C

C

OHOH

P CH2

HH H

H

OP

P

O

C

C C

C

OHOH

P CH2

HH H

H

NH2

N9 of base

3

O

C

C C

C

OHOH

P CH2

HH H

H

NH2N9 of Pu base

amine is now attachedin the configuration

this becomes the-glycosidic bond

PRPP amidotransferase

R5P

PRPP

5-phopho--ribosyl amine

inosine monophosphate

(ring assembly)

AMP

ADP

ATP

GMP

GDP

GTP

inhibitors of PRPPamidotransferse

Source of Purine Ring Constituents

N

N

N

N3

1

2

6

4

5 7

9

8

purine ring

4Purine Nucleotide Biosynthesis

10-formyl-tetrahydrofolate

N

N

N

N2HN

H

O H

H

N

CH2

R

5Purine Biosynthesis Pathway

PURINE PATHWAY

O

C

C C

C

OHOH

P CH2

HH H

H

OP

P

(5-phospho-ribosyl-1-pyrophosphate)

O

C

C C

C

OHOH

P CH2

HH H

H

NH2

amidophosphoribosyltransferase

GLN + H2O GLU + PPi

O

C

C C

C

OHOH

P CH2

HH H

H

NH

CO

CH2

NH2

glycinamide ribotide (GAR)

GAR synthetase

ADP + Pi

R5P

NH

O C

CH2

HN

ribose-5-phosphate(R5P)

CH

O

formylglycinamideribotide (FGAR)

GAR transformylase

N10-formyl-THF

THF

(tetrahydrofolates aremethyl/formyl donors)

NH

C

CH2

HN

R5P

CH

OHN

FGAM synthetase

AIR synthetase

ATP ADP + Pi

ATP + GLN

+ H20

ADP + GLU + Pi

6

5-aminoimidazole ribotide (AIR)

NC

HC

N

R5P

CH

H2N

5 memberimidazole

ring

NC

C

N

R5P

CH

H2N

O C

OAIR carboxylase

carboxyaminoimidazole ribotide

now have 4 membersof the 5 member ringATP

+

HCO3

ADP+Pi

NC

C

N

R5P

CH

H2N

C

O

CH

C O

O

NH

CCH2

O

O

CH

C O

O

NH

CCH2

O

O

5-aminoimidazole-4-(N-succinylocarboxamide)

ribotide (SACAIR)

ADP + Pi

ATP

5 of the 6 ring members

NC

C

N

R5P

CH

H2N

C

O

H2NCH

C O

O

C

CH

O

O

fumarate

SACAIRsynthetase

5-aminoimidazole-4-carboxamide ribotide

(AICAR)

adenylosuccinatelyase

THF

NC

C

N

R5P

CH

C

O

H2N

NH

CHO

N10-formyl-THF(formyl donor)

5-formaminoimidazole-4-carboxamide ribotide

(FAICAR)

AICAR transformylase

all 6 ringmembers

7

H2O

IMP cyclohydrolase

NC

C

N

CH

C

O

HN

NH

HC

O

C

C C

C

OHOH

P CH2

HH H

H

8

aspartate isthe N donor

glutamine isthe N donor

IMP is the precursorfor purine exocyclic

nt modifications

Pyrimidine Synthesis

Pyrimidine ring assembled attachment to the ribose sugar

O

N

N

43

2 6

5

1O

NH2

CO

O PO3

CH2

NH2

O

OH

C

C

O

OH

C

H

two components joined ring is closed

(precursor of UMP)

9

2 ATP + HCO3 + GLN + H2O carbamyl phosphateGLU

carbamyl phosphate synthetase II

PRPP and IMP (from PU synthesis)

pyrimidine nucleotides

Why not regulate Pu and Pyr synthesis at PRPP synthetase??

R5P PRPP PRPPsynthetase

5-phospho--ribosyl amine

Pu nts

PRPP amido transferase

Pyr ntscarbamyl PO4

synthetase II

The synthesis of carbamyl phosphate and regulation of pyrimidine biosynthesis

Why??

inhibitsinhibits

10Pyrimidine Biosynthesis

OA

OH OH

CH2PPP

OA

OH OH

CH2PP

H C OO

O

H2O

C

H

C O

O

NH3

CCH2 CH2

O

H2N

PYRIMIDINE PATHWAY

+

+

PO

NH2C O

P

C

H

C O

O

NH3

CCH2 CH2

O

HO

(building the Pyr ringstarting with carbonate)

(ATP supplies energy &

phosphate)

start with4 substrates

carbamoyl phosphatesynthetase

1

2

1

2

aspartate transcarbamylase

C

H

C O

O

NH3

CCH2

O

HO

C O

O

H

HO C

O

CH2

CH

NOC

NH2

P

constituents of Pyr are now joined

H2Odihydroorotase

(dehydration)

11

H

C O

O

H

C

O

CH2

CH

NOC

HNquinonereducedquinone

dihydroorotatedehydrogenase

C O

O

H

C

O

CH

C

NOC

HN

double bond formation

O

C

C C

C

OHOH

P CH2

HH H

H

OP

P

(5-phospho-ribosyl-1-pyrophosphate)

O

C

C C

C

OHOH

P CH2

HH H

orotate phosphoribosyl

transferase

C O

O

C

O

CH

C

NOC

HN

configuration

-configuration

in contrast to the purines, the base is synthesized before attachment to ribose

H

O

C

C C

C

OHOH

P CH2

HH H

C

O

CH

CH

NOC

HNOMP

decarboxylase

CO2

12

13two points concerning nucleotide biosynthesis

1.

2.

diphosphate / triphosphate synthesis

XMP XDP XTP

source of ATP

deoxyribonucleotide synthesis

ubiquitous enzyme found in all organisms

substrate

O

C

C C

C

OHOH

CH2

HH H

H

basePPO

C

C C

C

HOH

CH2

HH H

H

basePP

ribonucleotide reductase


XDPs

14ribonucleotide reductase “redox” rxn

(like cytochromes inoxidative phosphorylation)

ribonucleotide reductase recycled through a series of oxidation - reduction steps/rxns

ribonucleotide reductase (E. coli)

( XTP / XDP / XMP binding sites )

( inhibitors and activators of Pu and Pyr pathways )

NADPH

NADPoxidized

reducedthioredoxin

reduced

thioredoxin

oxidized

reduced



oxidized

nucleotide biosynthesis

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