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Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdA

Organism
Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
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 sitei9 – 91Allosteric activatorBy similarity
Binding sitei55 – 551Allosteric activatorBy similarity
Binding sitei91 – 911Allosteric activatorBy similarity
Binding sitei209 – 2091SubstrateBy similarity
Sitei225 – 2251Important for hydrogen atom transferBy similarity
Sitei232 – 2321Allosteric effector bindingBy similarity
Binding sitei253 – 2531Substrate; via amide nitrogenBy similarity
Sitei262 – 2621Allosteric effector bindingBy similarity
Active sitei437 – 4371Proton acceptorBy similarity
Active sitei439 – 4391Cysteine radical intermediateBy similarity
Active sitei441 – 4411Proton acceptorBy similarity
Sitei462 – 4621Important for hydrogen atom transferBy similarity
Sitei730 – 7301Important for electron transferBy similarity
Sitei731 – 7311Important for electron transferBy similarity
Sitei754 – 7541Interacts with thioredoxin/glutaredoxinBy similarity
Sitei759 – 7591Interacts 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

BioCyciBAPH224915:GJ9D-168-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:bbp_168
OrganismiBuchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
Taxonomic identifieri224915 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera
ProteomesiUP000000601: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 761761Ribonucleoside-diphosphate reductase subunit alphaPRO_0000187208Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi225 ↔ 462Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

STRINGi224915.bbp168.

Structurei

3D structure databases

ProteinModelPortaliQ89AS4.
SMRiQ89AS4. Positions 5-737.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini5 – 9591ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 217Allosteric activator bindingBy similarity
Regioni224 – 2252Substrate bindingBy similarity
Regioni437 – 4415Substrate bindingBy similarity
Regioni621 – 6255Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
KOiK00525.
OMAiHRFYDAT.
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.

Q89AS4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNQMLFVTKR NGKIELINLD KIHRVLNWAA KGLENISISQ VALKSRIQFY
60 70 80 90 100
NNIKTTIIHE TIIKAAADLI SENSPDYQYM AARLTIFHLR KKAFGQFNPP
110 120 130 140 150
NLYDHVKNMI KLEKYDQHLL NDYPKQDFLI MNSFIKHRRD MNFSYAAVKQ
160 170 180 190 200
LEGKYLIQNR VTKKIYESAQ FLYILISACL FSKYPNETRM KYIKNFYDAI
210 220 230 240 250
STFKISLPTP IMAGLRTPTR QFSSCVLIES EDNLNSINAT TSAIVKYVSQ
260 270 280 290 300
RAGIGINAGR IRALGSPIRN GDTLHTGCIP FYKHFQSAVK SCSQGGVRGG
310 320 330 340 350
AATIFYPIWH FEIESLLVLK NNRGIEENRV RHMDYSVQLN KLMYQRLILG
360 370 380 390 400
EHITLFSPSD VPNLYDSFFN NQEKFERLYI KYENDKTIRK KKVKASYLFS
410 420 430 440 450
LMMQERTSTG RIYIQNVDHC NSHSAFNPKI APIRQSNLCL EITLPTKALQ
460 470 480 490 500
DVHDKNGEIS LCTLSAINLG SLNNLNDLSK LSNLIVRALD SVLDYQEYPI
510 520 530 540 550
LSAKKSALSR RTLGIGVINF AYYLAKNGVR YSDGSANNLT HRTFEAIQYH
560 570 580 590 600
LLNASCVLAQ EKGACHWFSH TNYYKGILPI DTYKKNVDEI CNEPLHLDWE
610 620 630 640 650
LLRKKIKKYG LRNSTLSALM PSETSSQISN ATNGIEPPRG LISIKASKDG
660 670 680 690 700
MLRQVVPEYK RLKNNYELLW NIPNNTGYLQ LASIMQKFVD QSISANTNYD
710 720 730 740 750
PKLFPNNKIP MQQLILDLLT AYKLGLKTLY YQNTRDGASD HQTEDIQFSK
760
NENCNHGACK I
Length:761
Mass (Da):87,124
Last modified:June 1, 2003 - v1
Checksum:i7FB14E136283BDCF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA. Translation: AAO26901.1.
RefSeqiNP_777796.1. NC_004545.1.

Genome annotation databases

EnsemblBacteriaiAAO26901; AAO26901; bbp_168.
GeneIDi1058219.
KEGGibab:bbp168.
PATRICi21245113. VBIBucAph80364_0163.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE016826 Genomic DNA. Translation: AAO26901.1.
RefSeqiNP_777796.1. NC_004545.1.

3D structure databases

ProteinModelPortaliQ89AS4.
SMRiQ89AS4. Positions 5-737.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224915.bbp168.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO26901; AAO26901; bbp_168.
GeneIDi1058219.
KEGGibab:bbp168.
PATRICi21245113. VBIBucAph80364_0163.

Phylogenomic databases

eggNOGiCOG0209.
KOiK00525.
OMAiHRFYDAT.
OrthoDBiEOG6J48HC.

Enzyme and pathway databases

UniPathwayiUPA00326.
BioCyciBAPH224915:GJ9D-168-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: Bp.

Entry informationi

Entry nameiRIR1_BUCBP
AccessioniPrimary (citable) accession number: Q89AS4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 28, 2003
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 85 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.