NIFB_BRADU
ID NIFB_BRADU Reviewed; 499 AA.
AC P06770; Q9ANM2;
DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
DT 28-FEB-2003, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=FeMo cofactor biosynthesis protein NifB;
DE EC=4.-.-.-;
DE AltName: Full=Nitrogenase cofactor maturase NifB;
DE AltName: Full=Radical SAM assemblase NifB;
GN Name=nifB; OrderedLocusNames=blr1759;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=I110;
RX PubMed=3462181; DOI=10.1128/jb.167.3.774-783.1986;
RA Noti J.D., Folkerts O., Turken A.N., Szalay A.A.;
RT "Organization and characterization of genes essential for symbiotic
RT nitrogen fixation from Bradyrhizobium japonicum I110.";
RL J. Bacteriol. 167:774-783(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=USDA 110spc4;
RX PubMed=11157954; DOI=10.1128/jb.183.4.1405-1412.2001;
RA Goettfert M., Roethlisberger S., Kuendig C., Beck C., Marty R.,
RA Hennecke H.;
RT "Potential symbiosis-specific genes uncovered by sequencing a 410-kb DNA
RT region of the Bradyrhizobium japonicum chromosome.";
RL J. Bacteriol. 183:1405-1412(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
CC -!- FUNCTION: Involved in the biosynthesis of the iron-molybdenum cofactor
CC (FeMo-co or M-cluster) found in the dinitrogenase enzyme of the
CC nitrogenase complex in nitrogen-fixing microorganisms. NifB catalyzes
CC the crucial step of radical SAM-dependent carbide insertion that occurs
CC concomitant with the insertion of a 9th sulfur and the
CC rearrangement/coupling of two [4Fe-4S] clusters into a [8Fe-9S-C]
CC cluster, the precursor to the M-cluster.
CC {ECO:0000250|UniProtKB:D5VRM1}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000250|UniProtKB:D5VRM1};
CC Note=Binds 3 [4Fe-4S] clusters per monomer. One cluster is coordinated
CC with 3 cysteines and an exchangeable S-adenosyl-L-methionine. The two
CC others probably act as substrate. {ECO:0000250|UniProtKB:D5VRM1};
CC -!- PATHWAY: Cofactor biosynthesis; Fe-Mo cofactor biosynthesis.
CC {ECO:0000250|UniProtKB:D5VRM1}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. NifB family.
CC {ECO:0000305}.
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DR EMBL; M13688; AAA26221.1; -; Genomic_DNA.
DR EMBL; AF322012; AAG60744.1; -; Genomic_DNA.
DR EMBL; BA000040; BAC47024.1; -; Genomic_DNA.
DR PIR; A24495; A24495.
DR RefSeq; NP_768399.1; NC_004463.1.
DR AlphaFoldDB; P06770; -.
DR SMR; P06770; -.
DR STRING; 224911.27350012; -.
DR EnsemblBacteria; BAC47024; BAC47024; BAC47024.
DR KEGG; bja:blr1759; -.
DR PATRIC; fig|224911.5.peg.1784; -.
DR eggNOG; COG0535; Bacteria.
DR HOGENOM; CLU_027639_0_0_5; -.
DR InParanoid; P06770; -.
DR OMA; NHPCYSE; -.
DR PhylomeDB; P06770; -.
DR UniPathway; UPA00782; -.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009399; P:nitrogen fixation; IEA:UniProtKB-KW.
DR CDD; cd00852; NifB; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.30.420.130; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR003731; Di-Nase_FeMo-co_biosynth.
DR InterPro; IPR036105; DiNase_FeMo-co_biosyn_sf.
DR InterPro; IPR000385; MoaA_NifB_PqqE_Fe-S-bd_CS.
DR InterPro; IPR005980; Nase_CF_NifB.
DR InterPro; IPR034165; NifB_C.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR43787:SF3; PTHR43787:SF3; 1.
DR Pfam; PF02579; Nitro_FeMo-Co; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR SUPFAM; SSF53146; SSF53146; 1.
DR TIGRFAMs; TIGR01290; nifB; 1.
DR PROSITE; PS01305; MOAA_NIFB_PQQE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; Nitrogen fixation;
KW Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..499
FT /note="FeMo cofactor biosynthesis protein NifB"
FT /id="PRO_0000153037"
FT DOMAIN 49..298
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 63
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 69
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 70
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 117
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 169
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 221
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 294
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:D5VRM1"
FT BINDING 297
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:D5VRM1"
FT CONFLICT 20..22
FT /note="SCG -> RLR (in Ref. 1; AAA26221)"
FT /evidence="ECO:0000305"
FT CONFLICT 117
FT /note="G -> A (in Ref. 1; AAA26221)"
FT /evidence="ECO:0000305"
FT CONFLICT 295..298
FT /note="RQCR -> GSA (in Ref. 1; AAA26221)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 499 AA; 54897 MW; FE02B70C27853609 CRC64;
MQSITEHKGC RASAKTGRAS CGSQAGRGDL PVEIWERVKN HPCYSEDAHH HYARMHVAVA
PACNIQCNYC NRKYDCANES RPGVVSEKLT PEQAVRKVIA VATTIPQMTV LGIAGPGDAL
ANPAKTFKTL ALVTEAAPDI KLCLSTNGLA LPDYVDTIVR AKVDHVTITI NMVDPEIGAK
IYPWIFFNHK RYTGIEAARI LTNRQLQGLE MLSERGILCK INSVMIPNIN DDHLVEVNKA
VTSRGAFLHN IMPLISVPEH GTAFGLNGQR GPTAQELKTL QDACEGKINM MRHCRQCRAD
AVGLLGEDRS AEFTNDQVMK MDVHYDLEMR KAYQKRVENE RVSKVAAGQK ELAGVSGEMS
AITVLVAVAT KGSGLINEHF GHAKEFQLYE LSTSGAKFVG LRRVEGYCQA GYGEEDRLSV
IMRDIRDCHA VFVAKIGGCP KSGLIKAGIE PVDQFAYEYI EKSTIAWFRA YVGKVKRGEI
QHVQRGVPPR WPGDRISAA
