Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Vitamin B12-dependent ribonucleotide reductase

Gene

nrdJ

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
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 sitei153SubstrateBy similarity1
Binding sitei230Substrate; via amide nitrogenBy similarity1
Active sitei474Proton acceptorBy similarity1
Active sitei476Cysteine radical intermediateBy similarity1
Active sitei478Proton acceptorBy similarity1

GO - Molecular functioni

GO - Biological processi

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:bll4274
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
Proteomesi
  • UP000002526 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002316581 – 1254Vitamin B12-dependent ribonucleotide reductaseAdd BLAST1254

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi199 ↔ 487Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Interactioni

Protein-protein interaction databases

STRINGi224911.bll4274.

Structurei

3D structure databases

ProteinModelPortaliQ89MB9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni198 – 199Substrate bindingBy similarity2
Regioni474 – 478Substrate bindingBy similarity5
Regioni675 – 679Substrate bindingBy similarity5

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107RTZ. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000021770.
InParanoidiQ89MB9.
KOiK00525.
OMAiMTGVSYA.
OrthoDBiPOG091H0FGZ.
PhylomeDBiQ89MB9.

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
InterProiIPR017856. Integrase_Zn-bd_dom-like_N.
IPR013678. RNR_2_N.
IPR000788. RNR_lg_C.
IPR013344. RNR_NrdJ/NrdZ.
IPR029072. YebC-like.
[Graphical view]
PfamiPF08471. Ribonuc_red_2_N. 1 hit.
PF02867. Ribonuc_red_lgC. 2 hits.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF75625. SSF75625. 1 hit.
TIGRFAMsiTIGR02504. NrdJ_Z. 1 hit.

Sequencei

Sequence statusi: Complete.

Q89MB9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRIERRHTTT GQSPYAGIDF RLTTSEIRNP DGSVVFKLDN VEVPTEWSQV
60 70 80 90 100
ASDVLAQKYF RKAGVAARLK KVEEESVPSF LWRSVPDTEA LSQLPEKERY
110 120 130 140 150
VSELSAKQVF DRLAGCWTYW GWKGGYFTND EDAQAFYDEL RYMLAMQMVA
160 170 180 190 200
PNSPQWFNTG LHWAYGIDGP GQGHYYVDPF TGKLTKSKSA YEHPQPHACF
210 220 230 240 250
IQGVGDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSRLRG EGEKLSGGGR
260 270 280 290 300
SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDVDHPDI ETYIDWKVKE
310 320 330 340 350
EQKVAALVTG SKINQKHLKA VLKACVNCEG SGDDCFDPEK NPALRREIKL
360 370 380 390 400
ARRSLVPDNY IKRVIQFAKQ GYKDIQFDVY DTDWDSEAYL TVSGQNSNNS
410 420 430 440 450
VSLKDDFLRA VETDGDWNLN ARTSKKVTKT LKARDLWEKI GYAAWASADP
460 470 480 490 500
GLHFNTTMND WHTCKASGDI RASNPCSEYM FLDDTACNLA SANLLTFYNV
510 520 530 540 550
ATKHFDVEGY EHLCRLWTVV LEISVMMAQF PSKAIAELSY EFRTLGLGYA
560 570 580 590 600
NIGGLLMTMG LPYDSKEGRA LCGALTAVMT GITYKTSAEI AAELGTFPGY
610 620 630 640 650
KKNAAHMLRV IRNHRRAAHG QSNGYEALSV NPVPLDLVSC PQADLVSHAQ
660 670 680 690 700
AAWDAALELG EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK
710 720 730 740 750
KLAGGGYFKI INRAVPAALR ALGYRESEIA EIEAYAVGHG SLSNAPGINA
760 770 780 790 800
STLKAKGFTD EAIAKVEKAL PTAFDIKFAF NKWTFGEDFI RDQLGIGAEA
810 820 830 840 850
IAAPGFDLLQ AVGFTKREIE AANVHICGAM TVEGAPHLKA EHYPVFDCAN
860 870 880 890 900
PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCKSAYM
910 920 930 940 950
LSWKLALKAN ALYRDGSKLS QPLNSQLIAD DEDEDDAVES LYEKPMAART
960 970 980 990 1000
AQVSEKIVEK LVERIIVMRE REKMPDRRKG YTQKAVVGGH KVYLRTGEYD
1010 1020 1030 1040 1050
DGRLGEIFID MHKEGAALRS FINNFAIAVS LGLQYGVPLD EYVDAFTFTR
1060 1070 1080 1090 1100
FEPAGPVQGN DSIKYATSIL DYVFRELAVS YMSRFDLAHV DPTESNFDAL
1110 1120 1130 1140 1150
GKGVEEGKEP DEGHHASKLV SRGLTRSRTD NLVVMRGGST AVAQGNDSAP
1160 1170 1180 1190 1200
SGGSKVTALA SHGASARVGD VLEGAVALKQ EVSHDLSPTE KLEALQWSKS
1210 1220 1230 1240 1250
GTAQTLVPSK AERRAEAKAK GYEGEMCSEC GNFTLVRNGT CMKCDTCGST

TGCS
Length:1,254
Mass (Da):137,465
Last modified:June 1, 2003 - v1
Checksum:iFF888DB9EE21A33B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC49539.1.
RefSeqiNP_770914.1. NC_004463.1.
WP_011087047.1. NZ_CP011360.1.

Genome annotation databases

EnsemblBacteriaiBAC49539; BAC49539; BAC49539.
GeneIDi1053203.
KEGGibja:bll4274.
PATRICi21192088. VBIBraJap65052_4300.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC49539.1.
RefSeqiNP_770914.1. NC_004463.1.
WP_011087047.1. NZ_CP011360.1.

3D structure databases

ProteinModelPortaliQ89MB9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.bll4274.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC49539; BAC49539; BAC49539.
GeneIDi1053203.
KEGGibja:bll4274.
PATRICi21192088. VBIBraJap65052_4300.

Phylogenomic databases

eggNOGiENOG4107RTZ. Bacteria.
COG0209. LUCA.
HOGENOMiHOG000021770.
InParanoidiQ89MB9.
KOiK00525.
OMAiMTGVSYA.
OrthoDBiPOG091H0FGZ.
PhylomeDBiQ89MB9.

Family and domain databases

Gene3Di1.10.10.200. 1 hit.
InterProiIPR017856. Integrase_Zn-bd_dom-like_N.
IPR013678. RNR_2_N.
IPR000788. RNR_lg_C.
IPR013344. RNR_NrdJ/NrdZ.
IPR029072. YebC-like.
[Graphical view]
PfamiPF08471. Ribonuc_red_2_N. 1 hit.
PF02867. Ribonuc_red_lgC. 2 hits.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF75625. SSF75625. 1 hit.
TIGRFAMsiTIGR02504. NrdJ_Z. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiNRDJ_BRADU
AccessioniPrimary (citable) accession number: Q89MB9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: June 1, 2003
Last modified: November 30, 2016
This is version 89 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

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.