NIFB_HERSE
ID NIFB_HERSE Reviewed; 525 AA.
AC P27714;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 3.
DT 03-AUG-2022, entry version 99.
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;
OS Herbaspirillum seropedicae.
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Oxalobacteraceae; Herbaspirillum.
OX NCBI_TaxID=964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INDUCTION.
RC STRAIN=Z78 / ATCC 35893 / DSM 6446 / LMG 6514;
RX PubMed=17473889; DOI=10.1139/w06-085;
RA Rego F.G.M., Pedrosa F.O., Chubatsu L.S., Yates M.G.R., Wassem R.,
RA Steffens M.B., Rigo L.U., Souza E.M.;
RT "The expression of nifB gene from Herbaspirillum seropedicae is dependent
RT upon the NifA and RpoN proteins.";
RL Can. J. Microbiol. 52:1199-1207(2006).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-163.
RC STRAIN=Z78 / ATCC 35893 / DSM 6446 / LMG 6514;
RX PubMed=1840608; DOI=10.1099/00221287-137-7-1511;
RA Souza E.M., Funayama S., Rigo L.U., Yates M.G., Pedrosa F.O.;
RT "Sequence and structural organization of a nif A-like gene and part of a
RT nifB-like gene of Herbaspirillum seropedicae strain Z78.";
RL J. Gen. Microbiol. 137:1511-1522(1991).
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 -!- INDUCTION: Expression occurs only in the absence of ammonium and under
CC low levels of oxygen, and is strictly dependent on NifA.
CC {ECO:0000269|PubMed:17473889}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. NifB family.
CC {ECO:0000305}.
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DR EMBL; M60319; AAA25028.3; -; Genomic_DNA.
DR PIR; B44813; B44813.
DR AlphaFoldDB; P27714; -.
DR SMR; P27714; -.
DR UniPathway; UPA00782; -.
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 2: Evidence at transcript level;
KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; Nitrogen fixation;
KW S-adenosyl-L-methionine.
FT CHAIN 1..525
FT /note="FeMo cofactor biosynthesis protein NifB"
FT /id="PRO_0000153039"
FT DOMAIN 67..316
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT REGION 503..525
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 81
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 85
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 87
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 88
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 135
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 187
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250|UniProtKB:P69848"
FT BINDING 312
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:D5VRM1"
FT BINDING 315
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:D5VRM1"
SQ SEQUENCE 525 AA; 57440 MW; 9D4BCD8A3103F976 CRC64;
MQPTQYVGIQ DIKSLGTLLD KVAEHKGCGT SSEGGKASCG SSDGPADMAP EVWEKVKNHP
CYSEEAHHHY ARMHVAVAPA CNIQCNYCNR KYDCANESRP GVVSEKLTPE QAAKKVFAVA
STIPQMTVLG IAGPGDPLAN PAKTFKTFEL ISQTAPDIKL CLSTNGLALP DHIDTIAAFN
VDHVTITTNM VDPEIGQHIY PWIYYQNKRW TGIDAARILH ERQMLGLEML TARGILCKVN
SVMIPGINDQ HLVEVNRAVK SRGAFLHNIM PLISAPEHGT VFGLNGQRGP SAQELKALQD
ACEGEMNMMR HCRQCRADAV GLLGEDRSAE FTTEKIEAME VAYDGATRKA YQELVEQERQ
AKSAAKAAEQ QELAQMADQS GLSLLVAVAT KGQGRVNEHF GHVSEFQIYE VSSAGSKFVG
HRRVDQYCQG GYGEEDALET VIRAINDCHA VLVAKIGGCP KDDLQKVGIE PVDRYAHEFI
EQSVIAYFMD YLERVRSGQI EHRPRGDADI RQGAYTSVQS TSAAA
