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Protein

Vitamin B12-dependent ribonucleotide reductase

Gene

nrdJ

Organism
Rhodopirellula baltica (strain SH1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the reduction of ribonucleotides to deoxyribonucleotides. May function to provide a pool of deoxyribonucleotide precursors for DNA repair during oxygen limitation and/or for immediate growth after restoration of oxygen (By similarity).By similarity

Catalytic activityi

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

Cofactori

adenosylcob(III)alaminBy similarityNote: 5'-deoxyadenosylcobalamine (coenzyme B12).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei169 – 1691SubstrateBy similarity
Binding sitei242 – 2421Substrate; via amide nitrogenBy similarity
Active sitei420 – 4201Proton acceptorBy similarity
Active sitei422 – 4221Cysteine radical intermediateBy similarity
Active sitei424 – 4241Proton acceptorBy similarity

GO - Molecular functioni

  1. cobalamin binding Source: UniProtKB-KW
  2. cobalt ion binding Source: InterPro
  3. nucleotide binding Source: UniProtKB-KW
  4. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. DNA biosynthetic process Source: UniProtKB-KW
  2. DNA replication Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA synthesis

Keywords - Ligandi

Cobalamin, Cobalt, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Vitamin B12-dependent ribonucleotide reductase (EC:1.17.4.1)
Alternative name(s):
Ribonucleoside-diphosphate reductase NrdJ
Gene namesi
Name:nrdJ
Ordered Locus Names:RB12762
OrganismiRhodopirellula baltica (strain SH1)
Taxonomic identifieri243090 [NCBI]
Taxonomic lineageiBacteriaPlanctomycetesPlanctomycetiaPlanctomycetalesPlanctomycetaceaeRhodopirellula
ProteomesiUP000001025: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10401040Vitamin B12-dependent ribonucleotide reductasePRO_0000231655Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi214 ↔ 433Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi243090.RB12762.

Structurei

3D structure databases

ProteinModelPortaliQ7UI46.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni213 – 2142Substrate bindingBy similarity
Regioni420 – 4245Substrate bindingBy similarity
Regioni604 – 6085Substrate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000021771.
InParanoidiQ7UI46.
KOiK00525.
OMAiMTGVSYA.
OrthoDBiEOG6H4K5F.

Family and domain databases

InterProiIPR013678. RNR_2_N.
IPR000788. RNR_lg_C.
IPR013344. RNR_NrdJ/NrdZ.
IPR024434. TSCPD_dom.
[Graphical view]
PfamiPF08471. Ribonuc_red_2_N. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF12637. TSCPD. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
TIGRFAMsiTIGR02504. NrdJ_Z. 1 hit.

Sequencei

Sequence statusi: Complete.

Q7UI46-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTVLPESNA TSRIPANDPA LEKVDSEHGV EYAREKFGTA LRGDRAGLKF
60 70 80 90 100
ESKFCPDDGR TPFATTAWDL RSAAIKDESG NALFEQTDCE VPASWSQLAT
110 120 130 140 150
NVVVSKYFYG DPKNTDERER SVRQLIHRVT RTISDWGLAD GYFDTPEDGE
160 170 180 190 200
RFYRDLTWLS LHQHGAFNSP VWFNVGLHAQ YDVEGDMCNW HWDRTENTTA
210 220 230 240 250
QPDNPYEYPQ GSACFIQSVD DNMEDIMRLA CSEAMLFKFG SGTGTDLSTI
260 270 280 290 300
RSQREKLSGG GTPSGPLSFM RVYDSIAGVV KSGGKTRRAA KMQSLKVWHP
310 320 330 340 350
DILEFIECKW AEEKKAHALI REGYDSNFNG EAYASVCFQN ANLSVRLTDD
360 370 380 390 400
YMEAVRKNEN FQTRWITDKP TTEPPSYVAK ELLNKMAECA WHCGDPGVQY
410 420 430 440 450
DTTINKWHTC PNSGAINASN PCSEYMFLDD TACNLASINL MKFVQQDGSF
460 470 480 490 500
DHERFRAACR TFFIAQEILV DHASYPTEPI ARNSHKFRPL GLGYSNLGSV
510 520 530 540 550
IMTAGLPYDS DAARGMCGSL TALLHGEANR TSAELASVVG TFDGYVENEA
560 570 580 590 600
PMLRVMQMHR DACDQINDDG PAELKEAARE LWDGVLEIGE KYGFRNAQAT
610 620 630 640 650
VLAPTGTISF MMDCDTTGIE PDIALVKYKQ LAGGGMLKIV NQTVKLGLKT
660 670 680 690 700
LGYDADTIDE ILKYVDANDT IEGAPGLQDE HLAVFDCAFK PANGVRSIGW
710 720 730 740 750
RAHITMMAAA QPFLSGAISK TVNMPTDVTP QDIADAYFWG WELGLKAIAI
760 770 780 790 800
YRDGSKQSQP LNTKSDEQKA TDAAEAAKVE TVEKIVYKPR RERLPDTRQS
810 820 830 840 850
LTHKFSIAGH EGYLCVGLYP DGRPGEMFIT MAKEGSTIGG IMDSFGTALS
860 870 880 890 900
IAMQYGVPLE VIVNKFSHTR FEPMGHTSNK DIRIAKSVVD YIARWLGITF
910 920 930 940 950
MSGNDYSPSA EGAAKTGGNG PDLTTAPAGA TANNNSPVMA ELRADAGAAV
960 970 980 990 1000
ALVERATLLA SLQNGVSNGS ATNGHSNGQS AGGSSDGAVA ERAVDGLGGQ
1010 1020 1030 1040
ADQFSRFQTD APSCDNCGSI TVRNGNCYLC HNCGNSMGCS
Length:1,040
Mass (Da):113,464
Last modified:October 1, 2003 - v1
Checksum:iD640951F588F5C03
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX294155 Genomic DNA. Translation: CAD77768.1.
RefSeqiNP_870691.1. NC_005027.1.

Genome annotation databases

EnsemblBacteriaiCAD77768; CAD77768; RB12762.
GeneIDi1793559.
KEGGirba:RB12762.
PATRICi23253911. VBIRhoBal59814_6184.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX294155 Genomic DNA. Translation: CAD77768.1.
RefSeqiNP_870691.1. NC_005027.1.

3D structure databases

ProteinModelPortaliQ7UI46.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243090.RB12762.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAD77768; CAD77768; RB12762.
GeneIDi1793559.
KEGGirba:RB12762.
PATRICi23253911. VBIRhoBal59814_6184.

Phylogenomic databases

eggNOGiCOG0209.
HOGENOMiHOG000021771.
InParanoidiQ7UI46.
KOiK00525.
OMAiMTGVSYA.
OrthoDBiEOG6H4K5F.

Family and domain databases

InterProiIPR013678. RNR_2_N.
IPR000788. RNR_lg_C.
IPR013344. RNR_NrdJ/NrdZ.
IPR024434. TSCPD_dom.
[Graphical view]
PfamiPF08471. Ribonuc_red_2_N. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF12637. TSCPD. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
TIGRFAMsiTIGR02504. NrdJ_Z. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SH1.

Entry informationi

Entry nameiNRDJ_RHOBA
AccessioniPrimary (citable) accession number: Q7UI46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: October 1, 2003
Last modified: January 7, 2015
This is version 73 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

Complete proteome, Reference proteome

Documents

  1. 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.