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Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdA

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 4 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: DNA replication

This protein is involved in the pathway DNA replication, which is part of Genetic information processing.
View all proteins of this organism that are known to be involved in the pathway DNA replication and in Genetic information processing.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei7Allosteric activatorBy similarity1
Binding sitei52Allosteric activatorBy similarity1
Binding sitei88Allosteric activatorBy similarity1
Binding sitei219SubstrateBy similarity1
Sitei235Important for hydrogen atom transferBy similarity1
Sitei242Allosteric effector bindingBy similarity1
Binding sitei263Substrate; via amide nitrogenBy similarity1
Sitei272Allosteric effector bindingBy similarity1
Active sitei483Proton acceptorBy similarity1
Active sitei485Cysteine radical intermediateBy similarity1
Active sitei487Proton acceptorBy similarity1
Sitei521Important for hydrogen atom transferBy similarity1
Sitei783Important for electron transferBy similarity1
Sitei784Important for electron transferBy similarity1
Sitei796Interacts with thioredoxin/glutaredoxinBy similarity1
Sitei799Interacts with thioredoxin/glutaredoxinBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

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
Proteomesi
  • UP000000798 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001872051 – 801Ribonucleoside-diphosphate reductase subunit alphaAdd BLAST801

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
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)DescriptionActionsGraphical viewLength
Domaini3 – 92ATP-conePROSITE-ProRule annotationAdd BLAST90

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni13 – 19Allosteric activator bindingBy similarity7
Regioni234 – 235Substrate bindingBy similarity2
Regioni483 – 487Substrate bindingBy similarity5
Regioni680 – 684Substrate bindingBy similarity5

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000057034.
InParanoidiO66503.
KOiK00525.
OMAiIIAMTLM.
OrthoDBiPOG091H03NG.

Family and domain databases

InterProiIPR005144. ATP-cone_dom.
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:August 1, 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

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000057034.
InParanoidiO66503.
KOiK00525.
OMAiIIAMTLM.
OrthoDBiPOG091H03NG.

Enzyme and pathway databases

UniPathwayiUPA00326.

Family and domain databases

InterProiIPR005144. ATP-cone_dom.
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...

Entry informationi

Entry nameiRIR1_AQUAE
AccessioniPrimary (citable) accession number: O66503
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: November 2, 2016
This is version 114 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

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 one 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.