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Protein

Vitamin B12-dependent ribonucleotide reductase

Gene

nrdJ

Organism
Streptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

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.

Catalytic activityi

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

Cofactori

adenosylcob(III)alaminCuratedNote: 5'-deoxyadenosylcobalamine (coenzyme B12).Curated

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei143SubstrateBy similarity1
Binding sitei188Substrate; via amide nitrogenBy similarity1
Active sitei364Proton acceptorBy similarity1
Active sitei366Cysteine radical intermediateBy similarity1
Active sitei368Proton 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
OrganismiStreptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602)
Taxonomic identifieri443255 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002290281 – 961Vitamin B12-dependent ribonucleotide reductaseAdd BLAST961

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi160 ↔ 377Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Expressioni

Developmental stagei

Expressed during the exponential phase of growth.

Interactioni

Subunit structurei

Homotetramer.

Protein-protein interaction databases

STRINGi443255.SclaA2_010100022498.

Structurei

3D structure databases

ProteinModelPortaliO54196.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni159 – 160Substrate bindingBy similarity2
Regioni364 – 368Substrate bindingBy similarity5
Regioni554 – 558Substrate bindingBy similarity5

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.

Family and domain databases

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

Sequencei

Sequence statusi: Complete.

O54196-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTETTSGPAR GSRTKGTKAT KGLRIERVHT TPGVHPYDEV VWERRDVVMT
60 70 80 90 100
NWRDGSVNFE QRGVEFPDFW SVNAVNIVTS KYFRGAVGTP QRETGLKQLI
110 120 130 140 150
DRIVKTYRKA GEEYKYFASP ADAEIFEHEL AYALLHQIFS FNSPVWFNVG
160 170 180 190 200
TPQPQQVSAC FILSVDDSME SILDWYKEEG MIFKGGSGAG LNLSRIRSSK
210 220 230 240 250
ELLSSGGNAS GPVSFMRGAD ASAGTIKSGG ATRRAAKMVI LDVDHPDIEG
260 270 280 290 300
FIETKVKEEE KIRALRDAGF DMDLGGDDIT SVQYQNANNS VRVNDEFMRA
310 320 330 340 350
VESGSAFGLR ARMTGEIIEQ VDAKALFRKM AQAAWACADP GIQYDDTINR
360 370 380 390 400
WHTCPESGRI NGSNPCSEYM HLDNTSCNLA SLNLMKFLTD DGEGNQSFDV
410 420 430 440 450
ERFAKVVELV ITAMDISICF ADFPTQKIGE NTRAFRQLGI GYANLGALLM
460 470 480 490 500
ATGHAYDSDG GRAIAGAISS LMTGTSYRRS AELAAVVGPY DGYARNAAPH
510 520 530 540 550
NQVMRQHADA NDTAVRMDDL DTPIWAAATE TWQDVLRLGE KNGFRNAQAS
560 570 580 590 600
VIAPTGTIGL AMSCDTTGLE PDLALVKFKK LVGGGSMQIV NGTVPQALRR
610 620 630 640 650
LGYQAEQIEA IVEHIAEHGN VLDAPGLKTE HYKVFDCAMG ERSISAMGHV
660 670 680 690 700
RMMAAIQPWI SGALSKTVNM PESATVEEVE EIYFEAWKMG VKALAIYRDN
710 720 730 740 750
CKVGQPLSAK TKEKEQDGIA EKTEDTIRAA VEKVIEYRPV RKRLPKGRPG
760 770 780 790 800
ITTSFTVGGA EGYMTANSYP DDGLGEVFLK MSKQGSTLAG MMDAFSIAVS
810 820 830 840 850
VGLQYGVPLE TYVSKFTNMR FEPAGMTDDP DVRMAQSIVD NIFRRLALDF
860 870 880 890 900
LPFETRSALG IHSAEERQRH LDTGSYEQVI EEDELDVEGL AQSAPRQQIP
910 920 930 940 950
AVPAAPAEIP APKQAHTSAE LVEMQLGISA DAPLCFSCGT KMQRAGSCYI
960
CEGCGSTSGC S
Length:961
Mass (Da):104,791
Last modified:November 1, 1998 - v2
Checksum:i9C9D30730047A9F7
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ224870 Genomic DNA. Translation: CAA12167.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ224870 Genomic DNA. Translation: CAA12167.1.

3D structure databases

ProteinModelPortaliO54196.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi443255.SclaA2_010100022498.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105BZH. Bacteria.
COG0209. LUCA.

Family and domain databases

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

Entry informationi

Entry nameiNRDJ_STRC2
AccessioniPrimary (citable) accession number: O54196
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: November 1, 1998
Last modified: May 11, 2016
This is version 69 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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.