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Protein

FeMo cofactor biosynthesis protein NifB

Gene

nifB

Organism
Sinorhizobium fredii (strain NBRC 101917 / NGR234)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co or M-cluster) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing microorganisms. NifB catalyzes the crucial step of radical SAM-dependent carbide insertion that occurs concomitant with the insertion of a 9th sulfur and the rearrangement/coupling of two [4Fe-4S] clusters into a [8Fe-9S-C] cluster, the precursor to the M-cluster.By similarity

Cofactori

[4Fe-4S] clusterBy similarityNote: Binds 3 [4Fe-4S] clusters per monomer. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. The two others probably act as substrate.By similarity

Pathwayi: Fe-Mo cofactor biosynthesis

This protein is involved in the pathway Fe-Mo cofactor biosynthesis, which is part of Cofactor biosynthesis.By similarity
View all proteins of this organism that are known to be involved in the pathway Fe-Mo cofactor biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi76Iron-sulfur 1 (4Fe-4S-S-AdoMet)By similarity1
Metal bindingi80Iron-sulfur 1 (4Fe-4S-S-AdoMet)By similarity1
Binding sitei82S-adenosyl-L-methionineBy similarity1
Metal bindingi83Iron-sulfur 1 (4Fe-4S-S-AdoMet)By similarity1
Binding sitei130S-adenosyl-L-methionine; via carbonyl oxygenBy similarity1
Binding sitei182S-adenosyl-L-methionineBy similarity1
Binding sitei234S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygenBy similarity1
Metal bindingi307Iron-sulfur 2 (4Fe-4S)By similarity1
Metal bindingi310Iron-sulfur 2 (4Fe-4S)By similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase
Biological processNitrogen fixation
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

UniPathwayiUPA00782.

Names & Taxonomyi

Protein namesi
Recommended name:
FeMo cofactor biosynthesis protein NifB (EC:4.-.-.-)
Alternative name(s):
Nitrogenase cofactor maturase NifB
Radical SAM assemblase NifB
Gene namesi
Name:nifB
Ordered Locus Names:NGR_a01270
ORF Names:y4uM
Encoded oniPlasmid sym pNGR234a0 Publication
OrganismiSinorhizobium fredii (strain NBRC 101917 / NGR234)
Taxonomic identifieri394 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001054 Componenti: Plasmid sym pNGR234a

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001530461 – 493FeMo cofactor biosynthesis protein NifBAdd BLAST493

Structurei

3D structure databases

ProteinModelPortaliQ53205.
SMRiQ53205.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the radical SAM superfamily. NifB family.Curated

Phylogenomic databases

HOGENOMiHOG000225000.
KOiK02585.
OMAiNHPCYSE.
OrthoDBiPOG091H0IV4.

Family and domain databases

CDDicd00852. NifB. 1 hit.
Gene3Di3.20.20.70. 1 hit.
3.30.420.130. 1 hit.
InterProiView protein in InterPro
IPR013785. Aldolase_TIM.
IPR003731. Di-Nase_FeMo-co_biosynth.
IPR000385. MoaA_NifB_PqqE_Fe-S-bd_CS.
IPR005980. Nase_CF_NifB.
IPR034165. NifB_C.
IPR007197. rSAM.
PfamiView protein in Pfam
PF02579. Nitro_FeMo-Co. 1 hit.
PF04055. Radical_SAM. 1 hit.
SFLDiSFLDG01068. FeMo_cofactor_biosynthesis_pro. 1 hit.
SFLDS00029. Radical_SAM. 1 hit.
SUPFAMiSSF53146. SSF53146. 1 hit.
TIGRFAMsiTIGR01290. nifB. 1 hit.
PROSITEiView protein in PROSITE
PS01305. MOAA_NIFB_PQQE. 1 hit.

Sequencei

Sequence statusi: Complete.

Q53205-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSAPIISLES LTNTTSSGQL LTTAKSGGCA SSSCGSSSRP TDMDSATWEK
60 70 80 90 100
IKDHPCFSEE AHHYFARMHV AVAPACNIQC NYCNRKYDCA NESRPGVVSE
110 120 130 140 150
KLTPDQALRK VVAVANEVPQ LSVLGIAGPG DACYDWNKTR ATFERVASEI
160 170 180 190 200
PDIKLCISTN GLALPEHVDK LAEMNVSHVT ITINMVDPAV GEKIYPWIFY
210 220 230 240 250
GHRRYTGVDA AKILHEQQML GLEMLTARGI LTKINSVMIP GVNDLHLIEV
260 270 280 290 300
NKWVKERGAF LHNVMPLISD PAHGTSFGLT GQRGPNALEL KALHDRLEGG
310 320 330 340 350
AKLMRHCRQC RADAVGLLGT DRGQEFTLDH VPLEPHYDGA KRQAYREVVA
360 370 380 390 400
RIRDDHLEAK EKAIATVASA NIRGSLQVAV ATKGGGRINE HFGHAKEFQV
410 420 430 440 450
YEASQTGIKF VGHRKVEPYC HGGWGEDAAL AGIIAALDGI DIVLCARIGD
460 470 480 490
CPKERLMEAG IRATDTYGYD YIEAAISALH ATEFGTAPSQ ATA
Length:493
Mass (Da):53,507
Last modified:November 1, 1996 - v1
Checksum:i6C8F9A8F87E39AC8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z68203 Genomic DNA. Translation: CAA92412.1.
U00090 Genomic DNA. Translation: AAB91885.1.
RefSeqiNP_444098.1. NC_000914.2.
WP_010875165.1. NC_000914.2.

Genome annotation databases

EnsemblBacteriaiAAB91885; AAB91885; NGR_a01270.
GeneIDi962467.
KEGGirhi:NGR_a01270.
PATRICi32300951. VBIRhiSp122450_0111.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z68203 Genomic DNA. Translation: CAA92412.1.
U00090 Genomic DNA. Translation: AAB91885.1.
RefSeqiNP_444098.1. NC_000914.2.
WP_010875165.1. NC_000914.2.

3D structure databases

ProteinModelPortaliQ53205.
SMRiQ53205.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB91885; AAB91885; NGR_a01270.
GeneIDi962467.
KEGGirhi:NGR_a01270.
PATRICi32300951. VBIRhiSp122450_0111.

Phylogenomic databases

HOGENOMiHOG000225000.
KOiK02585.
OMAiNHPCYSE.
OrthoDBiPOG091H0IV4.

Enzyme and pathway databases

UniPathwayiUPA00782.

Family and domain databases

CDDicd00852. NifB. 1 hit.
Gene3Di3.20.20.70. 1 hit.
3.30.420.130. 1 hit.
InterProiView protein in InterPro
IPR013785. Aldolase_TIM.
IPR003731. Di-Nase_FeMo-co_biosynth.
IPR000385. MoaA_NifB_PqqE_Fe-S-bd_CS.
IPR005980. Nase_CF_NifB.
IPR034165. NifB_C.
IPR007197. rSAM.
PfamiView protein in Pfam
PF02579. Nitro_FeMo-Co. 1 hit.
PF04055. Radical_SAM. 1 hit.
SFLDiSFLDG01068. FeMo_cofactor_biosynthesis_pro. 1 hit.
SFLDS00029. Radical_SAM. 1 hit.
SUPFAMiSSF53146. SSF53146. 1 hit.
TIGRFAMsiTIGR01290. nifB. 1 hit.
PROSITEiView protein in PROSITE
PS01305. MOAA_NIFB_PQQE. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiNIFB_SINFN
AccessioniPrimary (citable) accession number: Q53205
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: March 15, 2017
This is version 99 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, Plasmid, Reference proteome

Documents

  1. Rhizobium plasmid pNGR234a
    Rhizobium plasmid pNGR234a: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. 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.