NIFB_METIM
ID NIFB_METIM Reviewed; 302 AA.
AC D5VRM1;
DT 15-FEB-2017, integrated into UniProtKB/Swiss-Prot.
DT 13-JUL-2010, sequence version 1.
DT 03-AUG-2022, entry version 54.
DE RecName: Full=FeMo cofactor biosynthesis protein NifB {ECO:0000303|PubMed:27268267};
DE EC=4.-.-.- {ECO:0000305};
DE AltName: Full=Nitrogenase cofactor maturase NifB {ECO:0000303|PubMed:27268267};
DE AltName: Full=Radical SAM assemblase NifB {ECO:0000303|PubMed:26969410};
GN Name=nifB {ECO:0000303|PubMed:27268267};
GN OrderedLocusNames=Metin_0554 {ECO:0000312|EMBL:ADG13224.1};
OS Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=573063;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 11812 / JCM 15783 / ME;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L.,
RA Pitluck S., Munk A.C., Detter J.C., Han C., Tapia R., Land M., Hauser L.,
RA Kyrpides N., Mikhailova N., Sieprawska-Lupa M., Whitman W.B., Woyke T.;
RT "Complete sequence of Methanocaldococcus infernus ME.";
RL Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP REVIEW.
RX PubMed=26969410; DOI=10.1016/j.cbpa.2016.02.016;
RA Hu Y., Ribbe M.W.;
RT "Maturation of nitrogenase cofactor-the role of a class E radical SAM
RT methyltransferase NifB.";
RL Curr. Opin. Chem. Biol. 31:188-194(2016).
RN [3]
RP FUNCTION, SAM CLEAVAGE, COFACTOR, PATHWAY, SUBUNIT, AND MUTAGENESIS OF
RP CYS-36; CYS-40; CYS-43; CYS-260 AND CYS-263.
RX PubMed=27268267; DOI=10.1021/jacs.6b03329;
RA Wilcoxen J., Arragain S., Scandurra A.A., Jimenez-Vicente E.,
RA Echavarri-Erasun C., Pollmann S., Britt R.D., Rubio L.M.;
RT "Electron paramagnetic resonance characterization of three iron-sulfur
RT clusters present in the nitrogenase cofactor maturase NifB from
RT Methanocaldococcus infernus.";
RL J. Am. Chem. Soc. 138:7468-7471(2016).
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
CC (PubMed:27268267). NifB catalyzes the crucial step of radical SAM-
CC dependent carbide insertion that occurs concomitant with the insertion
CC of a 9th sulfur and the rearrangement/coupling of two [4Fe-4S] clusters
CC into a [8Fe-9S-C] cluster, the precursor to the M-cluster
CC (PubMed:27268267, PubMed:26969410). {ECO:0000269|PubMed:27268267,
CC ECO:0000303|PubMed:26969410}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:27268267};
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:0000269|PubMed:27268267};
CC -!- PATHWAY: Cofactor biosynthesis; Fe-Mo cofactor biosynthesis.
CC {ECO:0000269|PubMed:27268267}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:27268267}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. NifB family.
CC {ECO:0000305}.
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DR EMBL; CP002009; ADG13224.1; -; Genomic_DNA.
DR RefSeq; WP_013099970.1; NC_014122.1.
DR AlphaFoldDB; D5VRM1; -.
DR SMR; D5VRM1; -.
DR STRING; 573063.Metin_0554; -.
DR EnsemblBacteria; ADG13224; ADG13224; Metin_0554.
DR GeneID; 9131560; -.
DR KEGG; mif:Metin_0554; -.
DR eggNOG; arCOG00956; Archaea.
DR HOGENOM; CLU_027639_1_0_2; -.
DR OMA; PCYNEKL; -.
DR OrthoDB; 46264at2157; -.
DR UniPathway; UPA00782; -.
DR Proteomes; UP000002061; 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 Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR005980; Nase_CF_NifB.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR43787:SF3; PTHR43787:SF3; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR SMART; SM00729; Elp3; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; Nitrogen fixation;
KW S-adenosyl-L-methionine.
FT CHAIN 1..302
FT /note="FeMo cofactor biosynthesis protein NifB"
FT /id="PRO_0000438991"
FT DOMAIN 22..264
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 36
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 ECO:0000305|PubMed:27268267"
FT BINDING 40
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 ECO:0000305|PubMed:27268267"
FT BINDING 43
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 ECO:0000305|PubMed:27268267"
FT BINDING 91
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 142
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 194
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 260
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:27268267"
FT BINDING 263
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:27268267"
FT MUTAGEN 36
FT /note="C->A: Loss of activity; when associated with A-40
FT and A-43."
FT /evidence="ECO:0000269|PubMed:27268267"
FT MUTAGEN 40
FT /note="C->A: Loss of activity; when associated with A-36
FT and A-43."
FT /evidence="ECO:0000269|PubMed:27268267"
FT MUTAGEN 43
FT /note="C->A: Loss of activity; when associated with A-36
FT and A-40."
FT /evidence="ECO:0000269|PubMed:27268267"
FT MUTAGEN 260
FT /note="C->A: Loss of activity; when associated with A-263."
FT /evidence="ECO:0000269|PubMed:27268267"
FT MUTAGEN 263
FT /note="C->A: Loss of activity; when associated with A-260."
FT /evidence="ECO:0000269|PubMed:27268267"
SQ SEQUENCE 302 AA; 35022 MW; F0603E857F9DBD44 CRC64;
MEKMSKFSHL LKAHPCFNEK VHDKYGRVHL PVAPRCNIAC KFCKRSVSKE CCEHRPGVSL
GVLKPEDVED YLKKILKEMP NIKVVGIAGP GDSLFNKETF ETLKIIDEKF PNLIKCISTN
GLLLSKYYKD LANLNVRTIT VTVNAIKPEI LEKIVDWVYY DKKLYRGLEG AKLLIEKQIE
GIKKASEEDF IIKINTVLIP EINMDHVVEI AKFFKDYAYV QNIIPLIPQY KMKELRAPTC
EEIKKVRKEC EKYIPQFRAC GQCRADAVGL IKEKELLKEF FKEKNKEKNI KLEVFDLKHF
SH
