DB code: M00203

CATH domain 3.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large Chain Catalytic domain
3.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large Chain Catalytic domain
3.-.-.- :
3.-.-.- :
E.C. 1.17.4.2 1.97.1.-
CSA 1b8b
M-CSA 1b8b
MACiE

CATH domain Related DB codes (homologues)
3.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large Chain S00247

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq
P07071 Anaerobic ribonucleoside-triphosphate reductase
EC 1.17.4.2
NP_049690.1 (Protein)
NC_000866.4 (DNA/RNA sequence)
P07075 Anaerobic ribonucleoside-triphosphate reductase-activating protein
EC 1.97.1.-
Class III anaerobic ribonucleotide reductase small component
NP_049688.1 (Protein)
NC_000866.4 (DNA/RNA sequence)

KEGG enzyme name
ribonucleoside-triphosphate reductase
(EC 1.17.4.2 )
ribonucleotide reductase
(EC 1.17.4.2 )
2'-deoxyribonucleoside-triphosphate:oxidized-thioredoxin2'-oxidoreductase
(EC 1.17.4.2 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07075 NRDG_BPT4 Tetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits. Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine (By similarity).
P07071 NRDD_BPT4 2''-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin. Tetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits.

KEGG Pathways
Map code Pathways E.C.
MAP00240 Pyrimidine metabolism 1.17.4.2
MAP00230 Purine metabolism 1.17.4.2

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00023 L00024 C00019 C03802 C00058 C04283 C00011 C00001
E.C.
Compound Iron [4Fe-4S] S-adenosyl-L-methionine Ribonucleoside triphosphate Formate 2'-Deoxyribonucleoside triphosphate CO2 H2O
Type heavy metal heavy metal,sulfide group amino acids,amine group,nucleoside,sulfonium ion nucleotide carboxyl group nucleotide others H2O
ChEBI 18248
82664
33725
67040
30751
16526
15377
PubChem 23925
34755
18971002
284
280
22247451
962
1b8bA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1h77A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Unbound Unbound Unbound Unbound Bound:2xDGT Unbound
1h78A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Bound:2xDCP Unbound
1h79A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Unbound Unbound Unbound Unbound Bound:2xTTP Unbound
1h7aA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FE2 Unbound Unbound Unbound Unbound Bound:DTP Unbound
1h7bA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1hk8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:_ZN Unbound Unbound Unbound Unbound Bound:2xDGT Unbound

Reference for Active-site residues
resource references E.C.
literature [11], [12], [19] & [22]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1b8bA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543; ; ; (Iron binding) ALA 580(Glycine radical, mutated) mutant G580A
1h77A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543;CYS 546;CYS 561;CYS 564(Iron binding) ALA 580(Glycine radical, mutated) mutant G580A
1h78A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543; ; ; (Iron binding) ALA 580(Glycine radical, mutated) mutant G580A, invisible 546-571
1h79A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543;CYS 546;CYS 561;CYS 564(Iron binding) ALA 580(Glycine radical, mutated) mutant G580A
1h7aA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543;CYS 546;CYS 561;CYS 564(Iron binding) ALA 580(Glycine radical, mutated) mutant G580A
1h7bA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543; ; ; (Iron binding) ALA 580(Glycine radical, mutated) mutant G580A, truncated 544-571
1hk8A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 78;CYS 79;CYS 290;ASN 311;GLU 446 CYS 543;CYS 546;CYS 561;CYS 564(Iron binding) ALA 580(Glycine radical, mutated) mutant G580A

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
Fig.1
[3]
Fig.2
[6]
[7]
Scheme 1, p.24222
[8]
p.722-724, p.728-729
[11]
p.1500-1503
[12]
Fig.3, Fig.4, p.R258-R260
[13]
Fig.1, Fig.2, p.733
[14]
[15]
[17]
Scheme 1
[18]
Scheme 2, p.6718-6719
[19]
SCHEME 1, SCHEME 2, p.40460-40462
[22]
Fig. 36, p.244-248
[23]
p.746-747
[25]
p.3830-3831

References
[1]
Resource
Comments
Medline ID
PubMed ID 8381402
Journal J Biol Chem
Year 1993
Volume 268
Pages 2296-9
Authors Mulliez E, Fontecave M, Gaillard J, Reichard P
Title An iron-sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 7929323
Journal J Biol Chem
Year 1994
Volume 269
Pages 26116-20
Authors Eliasson R, Pontis E, Eckstein F, Reichard P
Title Interactions of 2'-modified azido- and haloanalogs of deoxycytidine 5'-triphosphate with the anaerobic ribonucleotide reductase of Escherichia coli.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7669047
Journal Biochem Biophys Res Commun
Year 1995
Volume 214
Pages 28-35
Authors Eliasson R, Reichard P, Mulliez E, Ollagnier S, Fontecave M, Liepinsh E, Otting G
Title The mechanism of the anaerobic Escherichia coli ribonucleotide reductase investigated with nuclear magnetic resonance spectroscopy.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8621608
Journal J Biol Chem
Year 1996
Volume 271
Pages 9410-6
Authors Ollagnier S, Mulliez E, Gaillard J, Eliasson R, Fontecave M, Reichard P
Title The anaerobic Escherichia coli ribonucleotide reductase. Subunit structure and iron sulfur center.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8636106
Journal J Biol Chem
Year 1996
Volume 271
Pages 6827-31
Authors Sun X, Ollagnier S, Schmidt PP, Atta M, Mulliez E, Lepape L, Eliasson R, Graslund A, Fontecave M, Reichard P, Sjoberg BM
Title The free radical of the anaerobic ribonucleotide reductase from Escherichia coli is at glycine 681.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8702830
Journal J Biol Chem
Year 1996
Volume 271
Pages 20770-5
Authors Young P, Andersson J, Sahlin M, Sjoberg BM
Title Bacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580.
Related PDB
Related UniProtKB P07071
[7]
Resource
Comments
Medline ID
PubMed ID 9305874
Journal J Biol Chem
Year 1997
Volume 272
Pages 24216-23
Authors Ollagnier S, Mulliez E, Schmidt PP, Eliasson R, Gaillard J, Deronzier C, Bergman T, Graslund A, Reichard P, Fontecave M
Title Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11848913
Journal Chem Rev
Year 1998
Volume 98
Pages 705-762
Authors Stubbe J, van Der Donk WA
Title Protein Radicals in Enzyme Catalysis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10531327
Journal J Biol Chem
Year 1999
Volume 274
Pages 31291-6
Authors Tamarit J, Mulliez E, Meier C, Trautwein A, Fontecave M
Title The anaerobic ribonucleotide reductase from Escherichia coli. The small protein is an activating enzyme containing a [4fe-4s](2+) center.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10550691
Journal J Biol Inorg Chem
Year 1999
Volume 4
Pages 614-20
Authors Mulliez E, Ollagnier-de Choudens S, Meier C, Cremonini M, Luchinat C, Trautwein AX, Fontecave M
Title Iron-sulfur interconversions in the anaerobic ribonucleotide reductase from Escherichia coli.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
Medline ID 99165879
PubMed ID 10066165
Journal Science
Year 1999
Volume 283
Pages 1499-504
Authors Logan DT, Andersson J, Sjoberg BM, Nordlund P
Title A glycyl radical site in the crystal structure of a class III ribonucleotide reductase.
Related PDB
Related UniProtKB P07071
[12]
Resource
Comments
Medline ID
PubMed ID 10574800
Journal Structure Fold Des
Year 1999
Volume 7
Pages R257-62
Authors Eklund H, Fontecave M
Title Glycyl radical enzymes: a conservative structural basis for radicals.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11114511
Journal Curr Opin Struct Biol
Year 2000
Volume 10
Pages 731-6
Authors Stubbe J
Title Ribonucleotide reductases: the link between an RNA and a DNA world?
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10748010
Journal J Biol Chem
Year 2000
Volume 275
Pages 19449-55
Authors Andersson J, Westman M, Sahlin M, Sjoberg BM
Title Cysteines involved in radical generation and catalysis of class III anaerobic ribonucleotide reductase. A protein engineering study of bacteriophage T4 NrdD.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 10821845
Journal J Biol Chem
Year 2000
Volume 275
Pages 15669-75
Authors Tamarit J, Gerez C, Meier C, Mulliez E, Trautwein A, Fontecave M
Title The activating component of the anaerobic ribonucleotide reductase from Escherichia coli. An iron-sulfur center with only three cysteines.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 10644700
Journal J Biol Chem
Year 2000
Volume 275
Pages 2463-71
Authors Torrents E, Buist G, Liu A, Eliasson R, Kok J, Gibert I, Graslund A, Reichard P
Title The anaerobic (class III) ribonucleotide reductase from Lactococcus lactis. Catalytic properties and allosteric regulation of the pure enzyme system.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11297442
Journal Biochemistry
Year 2001
Volume 40
Pages 3730-6
Authors Mulliez E, Padovani D, Atta M, Alcouffe C, Fontecave M
Title Activation of class III ribonucleotide reductase by flavodoxin: a protein radical-driven electron transfer to the iron-sulfur center.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11389585
Journal Biochemistry
Year 2001
Volume 40
Pages 6713-9
Authors Padovani D, Thomas F, Trautwein AX, Mulliez E, Fontecave M
Title Activation of class III ribonucleotide reductase from E. coli. The electron transfer from the iron-sulfur center to S-adenosylmethionine.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11526118
Journal J Biol Chem
Year 2001
Volume 276
Pages 40457-63
Authors Andersson J, Bodevin S, Westman M, Sahlin M, Sjoberg BM
Title Two active site asparagines are essential for the reaction mechanism of the class III anaerobic ribonucleotide reductase from bacteriophage T4.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11266436
Journal J Biol Chem
Year 2001
Volume 276
Pages 9587-9
Authors Padovani D, Mulliez E, Fontecave M
Title Activation of class III ribonucleotide reductase by thioredoxin.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11427536
Journal J Biol Chem
Year 2001
Volume 276
Pages 33488-94
Authors Torrents E, Eliasson R, Wolpher H, Graslund A, Reichard P
Title The anaerobic ribonucleotide reductase from Lactococcus lactis. Interactions between the two proteins NrdD and NrdG.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11796141
Journal Prog Biophys Mol Biol
Year 2001
Volume 77
Pages 177-268
Authors Eklund H, Uhlin U, Farnegardh M, Logan DT, Nordlund P
Title Structure and function of the radical enzyme ribonucleotide reductase.
Related PDB
Related UniProtKB
[23]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11587648
Journal Structure (Camb)
Year 2001
Volume 9
Pages 739-50
Authors Larsson KM, Andersson J, Sjoberg BM, Nordlund P, Logan DT
Title Structural basis for allosteric substrate specificity regulation in anaerobic ribonucleotide reductases.
Related PDB 1b8b 1h77 1h78 1h79 1h7a 1h7b
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12107591
Journal J Mol Evol
Year 2002
Volume 55
Pages 138-52
Authors Torrents E, Aloy P, Gibert I, Rodriguez-Trelles F
Title Ribonucleotide reductases: divergent evolution of an ancient enzyme.
Related PDB
Related UniProtKB
[25]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS).
Medline ID
PubMed ID 12655046
Journal Proc Natl Acad Sci U S A
Year 2003
Volume 100
Pages 3826-31
Authors Logan DT, Mulliez E, Larsson KM, Bodevin S, Atta M, Garnaud PE, Sjoberg BM, Fontecave M
Title A metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase.
Related PDB 1hk8
Related UniProtKB P07071

Comments
This entry is for class III ribonucleotide reductase (anaerobic). Although other classes, I & II, of the enzymes uses a redoxin such as thioredoxin and glutaredoxin as a reductant, this enzyme uses formate (see [13] & [19]).
This enzyme forms tetramer consisting of 2 alpha (nrdD) and 2 beta (nrdG) subunits. Although the tertiary structure of the beta subunit (nrdG) has not been determined yet, its homodimer (beta2) binds a single [4Fe-4S] cluster and S-adenosyl-L-methionine as cofactors. Moreover, its sequence suggests that the beta subunit may adopt a half TIM-barrel structure (PDB;1r30, 1olt), which binds Fe-4S cluster and S-adenosyl-L-methionine. (Probably, the homodimer may be similar to a TIM-barrel structure.) On the other hand, the alpha subunit (nrdD) seems to be involved in generation of free radical at Gly 580.
This enzyme catalyzes radical reaction (see [11], [12], [13], [18] & [19]). The four-cysteine cluster (Cys543/Cys546,Cys561/Cys564), which might bind either iron or zinc in this enzyme, is descrived in the literature [25]. However, in any case, this cysteine cluster seems to be essential in the reaction (see [11], [14], [25]).
This enzyme catalyzes the following reactions (see [7], [11], [12], [13], [14], [15]):
(A) Electron transfer from reduced flavodoxin to [4Fe-4S] cluster of beta2 subunits (nrdG):
(B) Electron transfer from [4Fe-4S] cluster of beta2 subunits (nrdG) to S-adenosyl-L-Methionine (SAM or AdoMet) (nrdG):
(C) Radical formation at AdoMet, leading to formation of 5'-deoxyadenosyl radical and methionine (Radical cleavage):
The following reactions might proceed either by
(D) Radical transfer from 5'-deoxyadenosyl radical to Iron, bound to Cys543/Cys546/Cys561/Cys564 (nrdD), giving 5'-deoxyadenosine:
(E) Radical transfer from Iron, bound to Cys543/Cys546/Cys561/Cys564, to Gly580:
or by
(D') Radical transfer from 5'-deoxyadenosyl radical to Gly580 directly, giving 5'-deoxyadenosine (see [25]):
And then the following reactions occurs.
(F) Radical transfer from Gly580 to Cys290:
(G) Radical reactions at the active site:
###
Other classes are as follows:
Class I enzyme, described in entries, M00011, M00204 and M00205 (E.C. 1.17.4.1, R2 & R1 subunits).
Class II enzyme (e.g. adenocylcobalamine-dependent rebonucleotide reductase from Lactobacillus leichmannii, E.C 1.17.4.2).

Created Updated
2004-05-12 2009-02-26