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Protein

Vitamin B12-dependent ribonucleotide reductase

Gene

nrdJ

Organism
Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
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)DescriptionActionsGraphical viewLength
Binding sitei127SubstrateBy similarity1
Binding sitei200Substrate; via amide nitrogenBy similarity1
Active sitei376Proton acceptorBy similarity1
Active sitei378Cysteine radical intermediateBy similarity1
Active sitei380Proton acceptorBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processDNA synthesis
LigandCobalamin, 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:Bd1196
OrganismiBdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIB 9529 / HD100)
Taxonomic identifieri264462 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaOligoflexiaBdellovibrionalesBdellovibrionaceaeBdellovibrio
Proteomesi
  • UP000008080 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002316561 – 764Vitamin B12-dependent ribonucleotide reductaseAdd BLAST764

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi172 ↔ 389Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiQ6MNP6.

Interactioni

Protein-protein interaction databases

STRINGi264462.Bd1196.

Structurei

3D structure databases

ProteinModelPortaliQ6MNP6.
SMRiQ6MNP6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni171 – 172Substrate bindingBy similarity2
Regioni376 – 380Substrate bindingBy similarity5
Regioni561 – 565Substrate bindingBy similarity5

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000021771.
KOiK00525.
OMAiFIDRIND.
OrthoDBiPOG091H0FGZ.

Family and domain databases

CDDicd02888. RNR_II_dimer. 1 hit.
InterProiView protein in InterPro
IPR013678. RNR_2_N.
IPR000788. RNR_lg_C.
IPR013344. RNR_NrdJ/NrdZ.
PfamiView protein in Pfam
PF08471. Ribonuc_red_2_N. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PRINTSiPR01183. RIBORDTASEM1.
TIGRFAMsiTIGR02504. NrdJ_Z. 1 hit.

Sequencei

Sequence statusi: Complete.

Q6MNP6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKQTLHSPS YFVSGGKNPE SLFAWKNVNC EIRNRKGEVF FEMKNVEAPE
60 70 80 90 100
GWSQLAIDIA ASKYFRKVGV PKTGHETSVR QMVDRVVKAI VASAIRQGGY
110 120 130 140 150
FATRKEADIF AKELKFILLS QRGAFNSPVW FNAGLWEAYK AQSPSEHFAW
160 170 180 190 200
DEKKKSIQAT KNAYERPQCS ACFIQSVDDS IESIFDLAKT EAKLFKYGSG
210 220 230 240 250
TGSNFSKIRS KYEATGSGGK SSGLISFLEV LDKGAGAIKS GGTTRRAAKM
260 270 280 290 300
VVVDIDHPEV LDFIDWKMRE EQKAHLLIAA GLSADFEGEA YRTVSGQNAN
310 320 330 340 350
NSVRVSDAFM KAVEQERPWK LKARLTGKVL REIPAGEVWN RITRAAWMCA
360 370 380 390 400
DPGIQFHDTI NKWHTCPETD IIHSSNPCSE YMFLDDSACN LASINLVKFL
410 420 430 440 450
NDTGDFDFES FIHTARTLFV AQEILVDYSS YPTQRVAQNS HDYRPLGLGF
460 470 480 490 500
ANLGSLLMRK GVAYDSDEGR AWAGALTSLM SGVAYLTSSE MARAKGPFAG
510 520 530 540 550
YRKNSKSMLK VMKMHERALN QVAWKMLPAG IDKAVRNLWK GVLYNGEKYG
560 570 580 590 600
YRNAQATVIA PTGTIGLLMD CDTTGIEPDF SLIKFKKLVG GGEIQIVNQS
610 620 630 640 650
VDAALASLQY FEDERQAILK YVEENNSVVG APQMHPEDLP VFDTATAMPG
660 670 680 690 700
QRVLSPESHV KMMAAVQPFI SGAISKTVNM PSTATEEDIS RIYFLAWKLG
710 720 730 740 750
VKAVAVYRDG SKQSQPLNLK EKPKVVEEVG VPNFTMKCPE CGSDTVLTSG
760
CYRCPNCGTT VGCS
Length:764
Mass (Da):84,408
Last modified:July 5, 2004 - v1
Checksum:iB9B5369BEE85DB1E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX842649 Genomic DNA. Translation: CAE79105.1.
RefSeqiWP_011163707.1. NC_005363.1.

Genome annotation databases

EnsemblBacteriaiCAE79105; CAE79105; Bd1196.
KEGGibba:Bd1196.

Similar proteinsi

Entry informationi

Entry nameiNRDJ_BDEBA
AccessioniPrimary (citable) accession number: Q6MNP6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: July 5, 2004
Last modified: October 25, 2017
This is version 85 of the entry and version 1 of the sequence. See 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