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Q89MB9 (NRDJ_BRADU) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 77. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Vitamin B12-dependent ribonucleotide reductase

EC=1.17.4.1
Alternative name(s):
Ribonucleoside-diphosphate reductase NrdJ
Gene names
Name:nrdJ
Ordered Locus Names:bll4274
OrganismBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) [Reference proteome] [HAMAP]
Taxonomic identifier224911 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium

Protein attributes

Sequence length1254 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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.

Catalytic activity

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

Cofactor

5'-deoxyadenosylcobalamine (coenzyme B12) By similarity.

Sequence similarities

Belongs to the ribonucleoside diphosphate reductase class-2 family.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 12541254Vitamin B12-dependent ribonucleotide reductase
PRO_0000231658

Regions

Region198 – 1992Substrate binding By similarity
Region474 – 4785Substrate binding By similarity
Region675 – 6795Substrate binding By similarity

Sites

Active site4741Proton acceptor By similarity
Active site4761Cysteine radical intermediate By similarity
Active site4781Proton acceptor By similarity
Binding site1531Substrate By similarity
Binding site2301Substrate; via amide nitrogen By similarity

Amino acid modifications

Disulfide bond199 ↔ 487Redox-active By similarity

Sequences

Sequence LengthMass (Da)Tools
Q89MB9 [UniParc].

Last modified June 1, 2003. Version 1.
Checksum: FF888DB9EE21A33B

FASTA1,254137,465
        10         20         30         40         50         60 
MRIERRHTTT GQSPYAGIDF RLTTSEIRNP DGSVVFKLDN VEVPTEWSQV ASDVLAQKYF 

        70         80         90        100        110        120 
RKAGVAARLK KVEEESVPSF LWRSVPDTEA LSQLPEKERY VSELSAKQVF DRLAGCWTYW 

       130        140        150        160        170        180 
GWKGGYFTND EDAQAFYDEL RYMLAMQMVA PNSPQWFNTG LHWAYGIDGP GQGHYYVDPF 

       190        200        210        220        230        240 
TGKLTKSKSA YEHPQPHACF IQGVGDDLVN EGGIMDLWVR EARLFKYGSG TGSNFSRLRG 

       250        260        270        280        290        300 
EGEKLSGGGR SSGLMSFLKI GDRAAGAIKS GGTTRRAAKM VVVDVDHPDI ETYIDWKVKE 

       310        320        330        340        350        360 
EQKVAALVTG SKINQKHLKA VLKACVNCEG SGDDCFDPEK NPALRREIKL ARRSLVPDNY 

       370        380        390        400        410        420 
IKRVIQFAKQ GYKDIQFDVY DTDWDSEAYL TVSGQNSNNS VSLKDDFLRA VETDGDWNLN 

       430        440        450        460        470        480 
ARTSKKVTKT LKARDLWEKI GYAAWASADP GLHFNTTMND WHTCKASGDI RASNPCSEYM 

       490        500        510        520        530        540 
FLDDTACNLA SANLLTFYNV ATKHFDVEGY EHLCRLWTVV LEISVMMAQF PSKAIAELSY 

       550        560        570        580        590        600 
EFRTLGLGYA NIGGLLMTMG LPYDSKEGRA LCGALTAVMT GITYKTSAEI AAELGTFPGY 

       610        620        630        640        650        660 
KKNAAHMLRV IRNHRRAAHG QSNGYEALSV NPVPLDLVSC PQADLVSHAQ AAWDAALELG 

       670        680        690        700        710        720 
EKHGYRNAQT TVIAPTGTIG LVMDCDTTGI EPDFALVKFK KLAGGGYFKI INRAVPAALR 

       730        740        750        760        770        780 
ALGYRESEIA EIEAYAVGHG SLSNAPGINA STLKAKGFTD EAIAKVEKAL PTAFDIKFAF 

       790        800        810        820        830        840 
NKWTFGEDFI RDQLGIGAEA IAAPGFDLLQ AVGFTKREIE AANVHICGAM TVEGAPHLKA 

       850        860        870        880        890        900 
EHYPVFDCAN PCGKIGKRYL SVESHIRMMA AAQPFISGAI SKTINMPNDA TVEDCKSAYM 

       910        920        930        940        950        960 
LSWKLALKAN ALYRDGSKLS QPLNSQLIAD DEDEDDAVES LYEKPMAART AQVSEKIVEK 

       970        980        990       1000       1010       1020 
LVERIIVMRE REKMPDRRKG YTQKAVVGGH KVYLRTGEYD DGRLGEIFID MHKEGAALRS 

      1030       1040       1050       1060       1070       1080 
FINNFAIAVS LGLQYGVPLD EYVDAFTFTR FEPAGPVQGN DSIKYATSIL DYVFRELAVS 

      1090       1100       1110       1120       1130       1140 
YMSRFDLAHV DPTESNFDAL GKGVEEGKEP DEGHHASKLV SRGLTRSRTD NLVVMRGGST 

      1150       1160       1170       1180       1190       1200 
AVAQGNDSAP SGGSKVTALA SHGASARVGD VLEGAVALKQ EVSHDLSPTE KLEALQWSKS 

      1210       1220       1230       1240       1250 
GTAQTLVPSK AERRAEAKAK GYEGEMCSEC GNFTLVRNGT CMKCDTCGST TGCS 

« Hide

References

[1]"Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110."
Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S., Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M., Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.
DNA Res. 9:189-197(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
BA000040 Genomic DNA. Translation: BAC49539.1.
RefSeqNP_770914.1. NC_004463.1.

3D structure databases

ProteinModelPortalQ89MB9.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING224911.bll4274.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaBAC49539; BAC49539; BAC49539.
GeneID1053203.
KEGGbja:bll4274.
PATRIC21192088. VBIBraJap65052_4300.

Phylogenomic databases

eggNOGCOG0209.
HOGENOMHOG000021770.
KOK00525.
OrthoDBEOG6H4K5F.
PhylomeDBQ89MB9.

Enzyme and pathway databases

BioCycBJAP224911:GJEJ-4300-MONOMER.
RETL1328306-WGS:GSTH-1794-MONOMER.

Family and domain databases

InterProIPR013678. RNR_2_N.
IPR000788. RNR_lg_C.
IPR013344. RNR_NrdJ/NrdZ.
IPR024434. TSCPD_dom.
IPR029072. YebC-like.
[Graphical view]
PfamPF08471. Ribonuc_red_2_N. 1 hit.
PF02867. Ribonuc_red_lgC. 2 hits.
PF12637. TSCPD. 1 hit.
[Graphical view]
PRINTSPR01183. RIBORDTASEM1.
SUPFAMSSF75625. SSF75625. 1 hit.
TIGRFAMsTIGR02504. NrdJ_Z. 1 hit.
ProtoNetSearch...

Entry information

Entry nameNRDJ_BRADU
AccessionPrimary (citable) accession number: Q89MB9
Entry history
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: June 1, 2003
Last modified: July 9, 2014
This is version 77 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families