EzCatDB: M00203
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeM00203
CATH domainDomain 13.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large ChainCatalytic domain
Domain 23.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large ChainCatalytic domain
Domain 33.-.-.-
Domain 43.-.-.-
E.C.1.17.4.2,1.97.1.-
CSA1b8b

CATH domainRelated DB codes (homologues)
3.20.70.20 : Anaerobic Ribonucleotide-triphosphate Reductase Large ChainS00247

Enzyme Name
UniProtKBKEGG

P07071P07075
Protein nameAnaerobic ribonucleoside-triphosphate reductaseAnaerobic ribonucleoside-triphosphate reductase-activating proteinribonucleoside-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)

SynonymsEC 1.17.4.2
EC 1.97.1.-
Class III anaerobic ribonucleotide reductase small component
RefSeqNP_049690.1 (Protein)
NC_000866.4 (DNA/RNA sequence)
NP_049688.1 (Protein)
NC_000866.4 (DNA/RNA sequence)

KEGG pathways
MAP codePathwaysE.C.
MAP00230Purine metabolism1.17.4.2
MAP00240Pyrimidine metabolism1.17.4.2

UniProtKB:Accession NumberP07071P07075
Entry nameNRDD_BPT4NRDG_BPT4
Activity2''-deoxyribonucleoside triphosphate + thioredoxin disulfide + H(2)O = ribonucleoside triphosphate + thioredoxin.
SubunitTetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits.Tetramer consisting of 2 alpha (NrdD) and 2 beta (NrdG) subunits.
Subcellular location

Cofactor
Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00023L00024C00019C03802C00058C04283C00011C00001
CompoundIron[4Fe-4S]S-adenosyl-L-methionineRibonucleoside triphosphateFormate2'-Deoxyribonucleoside triphosphateCO2H2O
Typeheavy metalheavy metal,sulfide groupamino acids,amine group,nucleoside,sulfonium ionnucleotidecarboxyl groupnucleotideothersH2O
ChEBI18248
82664
33725
67040

30751

16526
15377
PubChem23925

34755

284
18971002

280
962
22247451
                
1b8bAUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1h77ABound:FE2UnboundUnboundUnboundUnboundBound:2xDGTUnbound 
1h78AUnboundUnboundUnboundUnboundUnboundBound:2xDCPUnbound 
1h79ABound:FE2UnboundUnboundUnboundUnboundBound:2xTTPUnbound 
1h7aABound:FE2UnboundUnboundUnboundUnboundBound:DTPUnbound 
1h7bAUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1hk8AAnalogue:_ZNUnboundUnboundUnboundUnboundBound:2xDGTUnbound 

Active-site residues
resource
literature [11], [12], [19] & [22]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
            
1b8bAASN 78;CYS 79;CYS 290;ASN 311;GLU 446
CYS 543;       ;       ;       (Iron binding)
ALA 580(Glycine radical, mutated)
mutant G580A
1h77AASN 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
1h78AASN 78;CYS 79;CYS 290;ASN 311;GLU 446
CYS 543;       ;       ;       (Iron binding)
ALA 580(Glycine radical, mutated)
mutant G580A, invisible 546-571
1h79AASN 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
1h7aAASN 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
1h7bAASN 78;CYS 79;CYS 290;ASN 311;GLU 446
CYS 543;       ;       ;       (Iron binding)
ALA 580(Glycine radical, mutated)
mutant G580A, truncated 544-571
1hk8AASN 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
ReferencesSectionsNo. 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]
PubMed ID8381402
JournalJ Biol Chem
Year1993
Volume268
Pages2296-9
AuthorsMulliez E, Fontecave M, Gaillard J, Reichard P
TitleAn iron-sulfur center and a free radical in the active anaerobic ribonucleotide reductase of Escherichia coli.
[2]
PubMed ID7929323
JournalJ Biol Chem
Year1994
Volume269
Pages26116-20
AuthorsEliasson R, Pontis E, Eckstein F, Reichard P
TitleInteractions of 2'-modified azido- and haloanalogs of deoxycytidine 5'-triphosphate with the anaerobic ribonucleotide reductase of Escherichia coli.
[3]
PubMed ID7669047
JournalBiochem Biophys Res Commun
Year1995
Volume214
Pages28-35
AuthorsEliasson R, Reichard P, Mulliez E, Ollagnier S, Fontecave M, Liepinsh E, Otting G
TitleThe mechanism of the anaerobic Escherichia coli ribonucleotide reductase investigated with nuclear magnetic resonance spectroscopy.
[4]
PubMed ID8621608
JournalJ Biol Chem
Year1996
Volume271
Pages9410-6
AuthorsOllagnier S, Mulliez E, Gaillard J, Eliasson R, Fontecave M, Reichard P
TitleThe anaerobic Escherichia coli ribonucleotide reductase. Subunit structure and iron sulfur center.
[5]
PubMed ID8636106
JournalJ Biol Chem
Year1996
Volume271
Pages6827-31
AuthorsSun X, Ollagnier S, Schmidt PP, Atta M, Mulliez E, Lepape L, Eliasson R, Graslund A, Fontecave M, Reichard P, Sjoberg BM
TitleThe free radical of the anaerobic ribonucleotide reductase from Escherichia coli is at glycine 681.
[6]
PubMed ID8702830
JournalJ Biol Chem
Year1996
Volume271
Pages20770-5
AuthorsYoung P, Andersson J, Sahlin M, Sjoberg BM
TitleBacteriophage T4 anaerobic ribonucleotide reductase contains a stable glycyl radical at position 580.
Related UniProtKBP07071
[7]
PubMed ID9305874
JournalJ Biol Chem
Year1997
Volume272
Pages24216-23
AuthorsOllagnier S, Mulliez E, Schmidt PP, Eliasson R, Gaillard J, Deronzier C, Bergman T, Graslund A, Reichard P, Fontecave M
TitleActivation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction.
[8]
PubMed ID11848913
JournalChem Rev
Year1998
Volume98
Pages705-762
AuthorsStubbe J, van Der Donk WA
TitleProtein Radicals in Enzyme Catalysis.
[9]
PubMed ID10531327
JournalJ Biol Chem
Year1999
Volume274
Pages31291-6
AuthorsTamarit J, Mulliez E, Meier C, Trautwein A, Fontecave M
TitleThe anaerobic ribonucleotide reductase from Escherichia coli. The small protein is an activating enzyme containing a [4fe-4s](2+) center.
[10]
PubMed ID10550691
JournalJ Biol Inorg Chem
Year1999
Volume4
Pages614-20
AuthorsMulliez E, Ollagnier-de Choudens S, Meier C, Cremonini M, Luchinat C, Trautwein AX, Fontecave M
TitleIron-sulfur interconversions in the anaerobic ribonucleotide reductase from Escherichia coli.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
Medline ID99165879
PubMed ID10066165
JournalScience
Year1999
Volume283
Pages1499-504
AuthorsLogan DT, Andersson J, Sjoberg BM, Nordlund P
TitleA glycyl radical site in the crystal structure of a class III ribonucleotide reductase.
Related UniProtKBP07071
[12]
PubMed ID10574800
JournalStructure Fold Des
Year1999
Volume7
PagesR257-62
AuthorsEklund H, Fontecave M
TitleGlycyl radical enzymes: a conservative structural basis for radicals.
[13]
PubMed ID11114511
JournalCurr Opin Struct Biol
Year2000
Volume10
Pages731-6
AuthorsStubbe J
TitleRibonucleotide reductases: the link between an RNA and a DNA world?
[14]
PubMed ID10748010
JournalJ Biol Chem
Year2000
Volume275
Pages19449-55
AuthorsAndersson J, Westman M, Sahlin M, Sjoberg BM
TitleCysteines involved in radical generation and catalysis of class III anaerobic ribonucleotide reductase. A protein engineering study of bacteriophage T4 NrdD.
[15]
PubMed ID10821845
JournalJ Biol Chem
Year2000
Volume275
Pages15669-75
AuthorsTamarit J, Gerez C, Meier C, Mulliez E, Trautwein A, Fontecave M
TitleThe activating component of the anaerobic ribonucleotide reductase from Escherichia coli. An iron-sulfur center with only three cysteines.
[16]
PubMed ID10644700
JournalJ Biol Chem
Year2000
Volume275
Pages2463-71
AuthorsTorrents E, Buist G, Liu A, Eliasson R, Kok J, Gibert I, Graslund A, Reichard P
TitleThe anaerobic (class III) ribonucleotide reductase from Lactococcus lactis. Catalytic properties and allosteric regulation of the pure enzyme system.
[17]
PubMed ID11297442
JournalBiochemistry
Year2001
Volume40
Pages3730-6
AuthorsMulliez E, Padovani D, Atta M, Alcouffe C, Fontecave M
TitleActivation of class III ribonucleotide reductase by flavodoxin: a protein radical-driven electron transfer to the iron-sulfur center.
[18]
PubMed ID11389585
JournalBiochemistry
Year2001
Volume40
Pages6713-9
AuthorsPadovani D, Thomas F, Trautwein AX, Mulliez E, Fontecave M
TitleActivation of class III ribonucleotide reductase from E. coli. The electron transfer from the iron-sulfur center to S-adenosylmethionine.
[19]
PubMed ID11526118
JournalJ Biol Chem
Year2001
Volume276
Pages40457-63
AuthorsAndersson J, Bodevin S, Westman M, Sahlin M, Sjoberg BM
TitleTwo active site asparagines are essential for the reaction mechanism of the class III anaerobic ribonucleotide reductase from bacteriophage T4.
[20]
PubMed ID11266436
JournalJ Biol Chem
Year2001
Volume276
Pages9587-9
AuthorsPadovani D, Mulliez E, Fontecave M
TitleActivation of class III ribonucleotide reductase by thioredoxin.
[21]
PubMed ID11427536
JournalJ Biol Chem
Year2001
Volume276
Pages33488-94
AuthorsTorrents E, Eliasson R, Wolpher H, Graslund A, Reichard P
TitleThe anaerobic ribonucleotide reductase from Lactococcus lactis. Interactions between the two proteins NrdD and NrdG.
[22]
PubMed ID11796141
JournalProg Biophys Mol Biol
Year2001
Volume77
Pages177-268
AuthorsEklund H, Uhlin U, Farnegardh M, Logan DT, Nordlund P
TitleStructure and function of the radical enzyme ribonucleotide reductase.
[23]
CommentsX-ray crystallography
PubMed ID11587648
JournalStructure (Camb)
Year2001
Volume9
Pages739-50
AuthorsLarsson KM, Andersson J, Sjoberg BM, Nordlund P, Logan DT
TitleStructural basis for allosteric substrate specificity regulation in anaerobic ribonucleotide reductases.
Related PDB1b8b,1h77,1h78,1h79,1h7a,1h7b
[24]
PubMed ID12107591
JournalJ Mol Evol
Year2002
Volume55
Pages138-52
AuthorsTorrents E, Aloy P, Gibert I, Rodriguez-Trelles F
TitleRibonucleotide reductases: divergent evolution of an ancient enzyme.
[25]
CommentsX-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS).
PubMed ID12655046
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages3826-31
AuthorsLogan DT, Mulliez E, Larsson KM, Bodevin S, Atta M, Garnaud PE, Sjoberg BM, Fontecave M
TitleA metal-binding site in the catalytic subunit of anaerobic ribonucleotide reductase.
Related PDB1hk8
Related UniProtKBP07071

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).

createdupdated
2004-05-122009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.