NIFB_RHIME
ID NIFB_RHIME Reviewed; 490 AA.
AC P09824;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 02-NOV-2001, sequence version 2.
DT 03-AUG-2022, entry version 132.
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=RA0442; ORFNames=SMa0814;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OG Plasmid pSymA (megaplasmid 1).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3029020; DOI=10.1128/jb.169.3.1120-1126.1987;
RA Buikema W.J., Klingensmith J.A., Gibbons S.L., Ausubel F.M.;
RT "Conservation of structure and location of Rhizobium meliloti and
RT Klebsiella pneumoniae nifB genes.";
RL J. Bacteriol. 169:1120-1126(1987).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481432; DOI=10.1073/pnas.161294798;
RA Barnett M.J., Fisher R.F., Jones T., Komp C., Abola A.P., Barloy-Hubler F.,
RA Bowser L., Capela D., Galibert F., Gouzy J., Gurjal M., Hong A., Huizar L.,
RA Hyman R.W., Kahn D., Kahn M.L., Kalman S., Keating D.H., Palm C.,
RA Peck M.C., Surzycki R., Wells D.H., Yeh K.-C., Davis R.W., Federspiel N.A.,
RA Long S.R.;
RT "Nucleotide sequence and predicted functions of the entire Sinorhizobium
RT meliloti pSymA megaplasmid.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9883-9888(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
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; M15544; AAA26306.1; -; Genomic_DNA.
DR EMBL; AE006469; AAK65100.1; -; Genomic_DNA.
DR PIR; A26951; A26951.
DR PIR; B95317; B95317.
DR RefSeq; NP_435688.1; NC_003037.1.
DR RefSeq; WP_010967430.1; NC_003037.1.
DR AlphaFoldDB; P09824; -.
DR SMR; P09824; -.
DR EnsemblBacteria; AAK65100; AAK65100; SMa0814.
DR GeneID; 61599253; -.
DR KEGG; sme:SMa0814; -.
DR PATRIC; fig|266834.11.peg.455; -.
DR HOGENOM; CLU_027639_0_0_5; -.
DR OMA; NHPCYSE; -.
DR UniPathway; UPA00782; -.
DR Proteomes; UP000001976; Plasmid pSymA.
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 SFLD; SFLDS00029; 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 Plasmid; Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..490
FT /note="FeMo cofactor biosynthesis protein NifB"
FT /id="PRO_0000153045"
FT DOMAIN 58..308
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 72
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 76
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 78
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 79
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 126
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 178
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 302
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:D5VRM1"
FT BINDING 305
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:D5VRM1"
FT CONFLICT 472..480
FT /note="GALYAAEFG -> ESSTPPSLA (in Ref. 1; AAA26306)"
FT /evidence="ECO:0000305"
FT CONFLICT 490
FT /note="A -> R (in Ref. 1; AAA26306)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 490 AA; 54224 MW; 29B7F595C5BB1BDB CRC64;
MSTPMILRES RTSTTFSDQL LENAKSVGCS PPSTAPGDID PGTWDKIKNH PCFSEEAHHY
FARMHVAVAP ACNIQCNYCN RKYDCANESR PGVASEKLTP DQAVRKVIAV ANEVPQLSVL
GIAGPGDACY DWKKTRATFE RVAREIPDIR LCISTNGLSL PDHVDELAEM NVDHVTITIN
MVDPRVGVKI YPWIYYGQRR HTGIDAARIL HERQMLGLEM LAERGILTKV NSVMIPGVND
EHLIEVNKVV KGRGALLHNV MPLISNRIHG TYYGLTGQRG PEAFELQALQ DRLEGTKLMR
HCRHCRADAI GLLGDDRGHE FTLAEIPDEI TYDASKRQAY RQLVARERGD HLVAKNEANR
TVMSVEYGGS LLIAVATKGG GRINEHFGHA KEFHVYTVSQ RGIKLAGRRR VEQYCLGGWG
EVATLDHIVV ALEGIDILLC VKIGDYPRKQ LTQAGLRATE AYGHDYIESA LGALYAAEFG
IEPPVKTATA
