SKFB_BACSU
ID SKFB_BACSU Reviewed; 410 AA.
AC O31423; O31424; O87096; O87097;
DT 11-JUL-2003, integrated into UniProtKB/Swiss-Prot.
DT 04-AUG-2003, sequence version 2.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Sporulation killing factor maturation protein SkfB;
DE EC=1.21.98.- {ECO:0000305|PubMed:23282011};
GN Name=skfB {ECO:0000303|PubMed:12817086}; Synonyms=ybcP, ybcQ;
GN OrderedLocusNames=BSU01920;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RA Haga K., Liu H., Yasumoto K., Takahashi H., Yoshikawa H.;
RT "Sequence analysis of the 70kb region between 17 and 23 degree of the
RT Bacillus subtilis chromosome.";
RL Submitted (JUL-1997) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP SEQUENCE REVISION.
RX PubMed=10568751; DOI=10.1101/gr.9.11.1116;
RA Medigue C., Rose M., Viari A., Danchin A.;
RT "Detecting and analyzing DNA sequencing errors: toward a higher quality of
RT the Bacillus subtilis genome sequence.";
RL Genome Res. 9:1116-1127(1999).
RN [4]
RP FUNCTION IN SYNTHESIS OF SKFA, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / PY79;
RX PubMed=12817086; DOI=10.1126/science.1086462;
RA Gonzalez-Pastor J.E., Hobbs E.C., Losick R.;
RT "Cannibalism by sporulating bacteria.";
RL Science 301:510-513(2003).
RN [5]
RP REPRESSION BY ABRB AND ABH.
RX PubMed=17720793; DOI=10.1128/jb.01081-07;
RA Strauch M.A., Bobay B.G., Cavanagh J., Yao F., Wilson A., Le Breton Y.;
RT "Abh and AbrB control of Bacillus subtilis antimicrobial gene expression.";
RL J. Bacteriol. 189:7720-7732(2007).
RN [6]
RP FUNCTION, SUBSTRATE SPECIFICITY, COFACTOR, AND MUTAGENESIS OF
RP 117-CYS--CYS-124 AND 380-CYS--CYS-387.
RC STRAIN=168;
RX PubMed=23282011; DOI=10.1021/ja310542g;
RA Fluehe L., Burghaus O., Wieckowski B.M., Giessen T.W., Linne U.,
RA Marahiel M.A.;
RT "Two [4Fe-4S] clusters containing radical SAM enzyme SkfB catalyze
RT thioether bond formation during the maturation of the sporulation killing
RT factor.";
RL J. Am. Chem. Soc. 135:959-962(2013).
CC -!- FUNCTION: Catalyzes the formation of the thioether bond required for
CC production of the sporulation killing factor (SKF) from SkfA
CC (PubMed:12817086). Forms the cysteine-methionine thioether bond found
CC in SKF; the acceptor amino acid can be hydrophobic, aromatic or a small
CC hydrophilic amino acid but not a larger hydrophilic amino acid, i.e.
CC Met=Ala, Phe, Leu, Tyr>Asn, Ser>>Gln, Glu, Lys (PubMed:23282011). The
CC relative position of Cys and Met in the substrate cannot be inverted,
CC in vitro the thioether bond cannot be made in the absence of the SkfA
CC propeptide, suggesting this is the first reaction in SKF maturation
CC (PubMed:23282011). In vitro, in the absence of a second substrate,
CC cleaves S-adenosyl-L-methionine into Met and 5'-dA (PubMed:23282011).
CC {ECO:0000269|PubMed:12817086, ECO:0000269|PubMed:23282011}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:23282011};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine
CC (PubMed:23282011). The other is coordinated via 3 cysteines and maybe
CC direct contact with the SkfA precursor (Probable).
CC {ECO:0000269|PubMed:23282011, ECO:0000305|PubMed:23282011};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:23282011}.
CC -!- INDUCTION: By Spo0A (PubMed:12817086) and PhoP, during nutrient
CC starvation, especially phosphate starvation. Repressed by AbrB during
CC normal growth when nutrients are plentiful, in association with the
CC transcriptional repressor Abh. {ECO:0000269|PubMed:12817086,
CC ECO:0000269|PubMed:17720793}.
CC -!- DISRUPTION PHENOTYPE: When the skfA-skfB-skfC-skfE-skfF-skfG-skfH
CC operon is deleted, increased rate of spore formation; a double operon
CC deletion (sdpA-sdpC plus skfA-skfH) makes spores even faster
CC (PubMed:12817086). {ECO:0000269|PubMed:12817086}.
CC -!- MISCELLANEOUS: Accelerated cannibalism by skf- cells is seen on solid
CC media but not in liquid media. {ECO:0000269|PubMed:12817086}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA33089.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AB006424; BAA33087.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AB006424; BAA33088.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AB006424; BAA33089.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AL009126; CAB11985.2; -; Genomic_DNA.
DR PIR; D69746; D69746.
DR PIR; E69746; E69746.
DR RefSeq; NP_388073.2; NC_000964.3.
DR RefSeq; WP_003234902.1; NZ_JNCM01000030.1.
DR PDB; 6EFN; X-ray; 1.29 A; A=1-410.
DR PDBsum; 6EFN; -.
DR AlphaFoldDB; O31423; -.
DR SMR; O31423; -.
DR STRING; 224308.BSU01920; -.
DR PaxDb; O31423; -.
DR PRIDE; O31423; -.
DR DNASU; 938501; -.
DR EnsemblBacteria; CAB11985; CAB11985; BSU_01920.
DR GeneID; 938501; -.
DR KEGG; bsu:BSU01920; -.
DR PATRIC; fig|224308.179.peg.199; -.
DR eggNOG; COG0535; Bacteria.
DR InParanoid; O31423; -.
DR OMA; TYFEGQM; -.
DR PhylomeDB; O31423; -.
DR BioCyc; BSUB:BSU01920-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0030152; P:bacteriocin biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR023885; 4Fe4S-binding_SPASM_dom.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR000385; MoaA_NifB_PqqE_Fe-S-bd_CS.
DR InterPro; IPR007197; rSAM.
DR InterPro; IPR030915; rSAM_SkfB.
DR Pfam; PF04055; Radical_SAM; 1.
DR Pfam; PF13186; SPASM; 1.
DR SFLD; SFLDF00515; sporulation_killing_factor_pro; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR04403; rSAM_skfB; 1.
DR PROSITE; PS01305; MOAA_NIFB_PQQE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Antibiotic biosynthesis; Bacteriocin biosynthesis;
KW Cytoplasm; Iron; Iron-sulfur; Metal-binding; Oxidoreductase;
KW Reference proteome; S-adenosyl-L-methionine.
FT CHAIN 1..410
FT /note="Sporulation killing factor maturation protein SkfB"
FT /id="PRO_0000153049"
FT DOMAIN 103..314
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 117
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:0000305|PubMed:23282011"
FT BINDING 121
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:0000305|PubMed:23282011"
FT BINDING 124
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:0000305|PubMed:23282011"
FT BINDING 380
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-substrate"
FT /evidence="ECO:0000305|PubMed:23282011"
FT BINDING 385
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-substrate"
FT /evidence="ECO:0000305|PubMed:23282011"
FT BINDING 387
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /ligand_note="4Fe-4S-S-substrate"
FT /evidence="ECO:0000305|PubMed:23282011"
FT MUTAGEN 117..124
FT /note="CNLSCSFC->ANLSASFA: No longer cleaves SAM, contains
FT 55% iron of wild-type."
FT /evidence="ECO:0000269|PubMed:23282011"
FT MUTAGEN 380..387
FT /note="CEAKNCKC->AEAKNAKA: Cleaves SAM, but does not form
FT thioether bond, contains 52% iron of wild-type."
FT /evidence="ECO:0000269|PubMed:23282011"
FT STRAND 14..19
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 22..27
FT /evidence="ECO:0007829|PDB:6EFN"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 38..50
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 53..64
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 70..77
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 81..85
FT /evidence="ECO:0007829|PDB:6EFN"
FT TURN 86..91
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 138..150
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 155..162
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 163..165
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 169..179
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 180..187
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 194..203
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 205..211
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 216..223
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 228..241
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 246..252
FT /evidence="ECO:0007829|PDB:6EFN"
FT TURN 254..256
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 260..270
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 273..279
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 284..287
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 295..312
FT /evidence="ECO:0007829|PDB:6EFN"
FT TURN 313..315
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:6EFN"
FT TURN 336..338
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 339..342
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 346..351
FT /evidence="ECO:0007829|PDB:6EFN"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:6EFN"
FT TURN 361..363
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 366..369
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 372..381
FT /evidence="ECO:0007829|PDB:6EFN"
FT HELIX 388..390
FT /evidence="ECO:0007829|PDB:6EFN"
SQ SEQUENCE 410 AA; 45755 MW; 3D243C673E811C0F CRC64;
MSYDRVKDFD LPELAVHLQP HGAVMIDRKS MFYFRLSGRG AQLAFLLSKN KNLHKTARIW
EIMKKEEMSA DQLKEELSAH PFTEAWTEGL LDQPLHVSGS LDSYLPISCT LQLTNACNLS
CSFCYASSGK PYPEELSSEQ WILVMQKLAA HGVADITLTG GEAKLIKGFK ELVVVASSLF
TNVNVFSNGL NWRDEEVELL SHLGNVSVQI SIDGMDNTHD QLRGRKGGFK ESMNTIKKLS
EANIPVIVAM TINESNADEV SDVVEQCANA GAFIFRAGKT LSVGRATEGF KALDIDFEEM
VQIQLREARH KWGDRLNIID WEHEESSFTT DFCTPGYLAW YIRADGYVTP CQLEDLPLGH
ILEDSMADIG SPARLLQLKC EAKNCKCIGK IELSEPDLPF QKEVKAGIQE
