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Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdA

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).By similarity

Catalytic activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

Enzyme regulationi

Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the alpha subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site (By similarity).By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei7 – 71Allosteric activatorBy similarity
Binding sitei52 – 521Allosteric activatorBy similarity
Binding sitei88 – 881Allosteric activatorBy similarity
Binding sitei219 – 2191SubstrateBy similarity
Sitei235 – 2351Important for hydrogen atom transferBy similarity
Sitei242 – 2421Allosteric effector bindingBy similarity
Binding sitei263 – 2631Substrate; via amide nitrogenBy similarity
Sitei272 – 2721Allosteric effector bindingBy similarity
Active sitei483 – 4831Proton acceptorBy similarity
Active sitei485 – 4851Cysteine radical intermediateBy similarity
Active sitei487 – 4871Proton acceptorBy similarity
Sitei521 – 5211Important for hydrogen atom transferBy similarity
Sitei783 – 7831Important for electron transferBy similarity
Sitei784 – 7841Important for electron transferBy similarity
Sitei796 – 7961Interacts with thioredoxin/glutaredoxinBy similarity
Sitei799 – 7991Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-77-MONOMER.
UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase subunit alpha (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase
Gene namesi
Name:nrdA
Ordered Locus Names:aq_094
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
ProteomesiUP000000798 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 801801Ribonucleoside-diphosphate reductase subunit alphaPRO_0000187205Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi235 ↔ 521Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

STRINGi224324.aq_094.

Structurei

3D structure databases

ProteinModelPortaliO66503.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 9290ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni13 – 197Allosteric activator bindingBy similarity
Regioni234 – 2352Substrate bindingBy similarity
Regioni483 – 4875Substrate bindingBy similarity
Regioni680 – 6845Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057034.
InParanoidiO66503.
KOiK00525.
OMAiRTHDLFT.
OrthoDBiEOG6J48HC.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O66503-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMYVIKRSG RKEKLDINKI RIAIKFACEG LNVDPLELEA DAQIQFRDGI
60 70 80 90 100
TTKEIQQLLI KTAAEKVSAE RPDWTYTAAR LLLYDLYKDV AHLRGYSLRD
110 120 130 140 150
DLGKYKPYNR KNFYSFVKEY VEKGIYGEYL LENYSEEDFN KLANYIKPER
160 170 180 190 200
DLYFTYTGIK ILYDRYLVRD EEGRVIELPQ EMYMLIAMTL AVPEKPEERL
210 220 230 240 250
KWAKKFYDVL SEHKVTVATP TLMNARRPFT QLSSCFVLTV DDDLFDIFDN
260 270 280 290 300
VKKAGMISKF AGGLGVYLGK IRATGAPIRK FKGASSGVIP VVKLINDTMT
310 320 330 340 350
YVDQLGMRKG SASITLDIWH KDILDFLEVK TNVGDERKKA HDIHPAVSIP
360 370 380 390 400
DLFMKRLKNR EDWTLIDPYW ARQYITRKIY DGKYKEVKPL PGSHYYVGIK
410 420 430 440 450
EDGTQDILEP KGLEDFYGEE FEKWYLELEE NLPSYAKKKV NSFELWKRLL
460 470 480 490 500
TVAFETGEPY IFFRDEANRK NPNKHTGMVY SSNLCHEIVQ TMSPSKHEKP
510 520 530 540 550
VLDPETGEIT YKKEAGDLPV CNLGSVNLGK VHTEEEIKEV LPLLVRMLDN
560 570 580 590 600
VIEMNFYAIP EAEYTNKRYR AIGIGVSNYH YCLVKNGIKW ESEEHLKFAD
610 620 630 640 650
KLFELIAFYA LKGSLELAKE RGRYKLFDGS NWSKGILFGR SVEEIEENSR
660 670 680 690 700
QNGNNLPWRE LAEEIKKYGI RNAYLLALMP TGSTSLILGA TPSIDPIFAR
710 720 730 740 750
FYKEENMSGI LPQVPPEVDR FYWHYKTAYT IDHEWTIRAA AVRQKWIDQA
760 770 780 790 800
QSLNLFVDPQ NIDGPRLSRL YELAWELGLK TIYYLRSRSA MDIEECEACS

V
Length:801
Mass (Da):92,914
Last modified:July 31, 1998 - v1
Checksum:iFF728EDC7D97C396
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06460.1.
PIRiD70309.
RefSeqiNP_213062.1. NC_000918.1.
WP_010880000.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC06460; AAC06460; aq_094.
GeneIDi1192514.
KEGGiaae:aq_094.
PATRICi20957884. VBIAquAeo85532_0082.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC06460.1.
PIRiD70309.
RefSeqiNP_213062.1. NC_000918.1.
WP_010880000.1. NC_000918.1.

3D structure databases

ProteinModelPortaliO66503.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_094.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC06460; AAC06460; aq_094.
GeneIDi1192514.
KEGGiaae:aq_094.
PATRICi20957884. VBIAquAeo85532_0082.

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000057034.
InParanoidiO66503.
KOiK00525.
OMAiRTHDLFT.
OrthoDBiEOG6J48HC.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciAAEO224324:GJBH-77-MONOMER.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VF5.

Entry informationi

Entry nameiRIR1_AQUAE
AccessioniPrimary (citable) accession number: O66503
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 29, 2000
Last sequence update: July 31, 1998
Last modified: March 31, 2015
This is version 107 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.