LYTF_BACSU
ID LYTF_BACSU Reviewed; 488 AA.
AC O07532;
DT 16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 2.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Peptidoglycan endopeptidase LytF;
DE EC=3.4.-.-;
DE AltName: Full=Autolysin LytF;
DE AltName: Full=Cell wall-associated polypeptide CWBP49';
DE AltName: Full=Gamma-D-glutamate-meso-diaminopimelate muropeptidase LytF;
DE AltName: Full=Peptidoglycan hydrolase LytF;
DE AltName: Full=Vegetative cell wall hydrolase LytF;
DE Flags: Precursor;
GN Name=lytF; Synonyms=cwlE, yhdD; OrderedLocusNames=BSU09370;
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;
RX PubMed=9579061; DOI=10.1099/00221287-144-4-859;
RA Noback M.A., Holsappel S., Kiewiet R., Terpstra P., Wambutt R., Wedler H.,
RA Venema G., Bron S.;
RT "The 172 kb prkA-addAB region from 83 degrees to 97 degrees of the Bacillus
RT subtilis chromosome contains several dysfunctional genes, the glyB marker,
RT many genes encoding transporter proteins, and the ubiquitous hit gene.";
RL Microbiology 144:859-875(1998).
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 TO 87.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [4]
RP PROTEIN SEQUENCE OF 27-37, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, PH DEPENDENCE, INDUCTION, AND SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=10206711; DOI=10.1099/13500872-145-1-57;
RA Margot P., Pagni M., Karamata D.;
RT "Bacillus subtilis 168 gene lytF encodes a gamma-D-glutamate-meso-
RT diaminopimelate muropeptidase expressed by the alternative vegetative sigma
RT factor, sigma-D.";
RL Microbiology 145:57-65(1999).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, INDUCTION, AND DOMAIN.
RC STRAIN=168;
RX PubMed=10322020; DOI=10.1128/jb.181.10.3178-3184.1999;
RA Ohnishi R., Ishikawa S., Sekiguchi J.;
RT "Peptidoglycan hydrolase LytF plays a role in cell separation with CwlF
RT during vegetative growth of Bacillus subtilis.";
RL J. Bacteriol. 181:3178-3184(1999).
RN [6]
RP SUBCELLULAR LOCATION.
RC STRAIN=168;
RX PubMed=14594841; DOI=10.1128/jb.185.22.6666-6677.2003;
RA Yamamoto H., Kurosawa S., Sekiguchi J.;
RT "Localization of the vegetative cell wall hydrolases LytC, LytE, and LytF
RT on the Bacillus subtilis cell surface and stability of these enzymes to
RT cell wall-bound or extracellular proteases.";
RL J. Bacteriol. 185:6666-6677(2003).
RN [7]
RP FUNCTION IN CELL SEPARATION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168 / PY79, and 3610;
RX PubMed=19542270; DOI=10.1128/jb.00521-09;
RA Chen R., Guttenplan S.B., Blair K.M., Kearns D.B.;
RT "Role of the sigmaD-dependent autolysins in Bacillus subtilis population
RT heterogeneity.";
RL J. Bacteriol. 191:5775-5784(2009).
CC -!- FUNCTION: Cell wall hydrolase that cleaves gamma-D-glutamate-meso-
CC diaminopimelate bonds in peptidoglycan. LytF is necessary and
CC sufficient for vegetative daughter cell separation, and also seems to
CC play a role in cell autolysis. {ECO:0000269|PubMed:10206711,
CC ECO:0000269|PubMed:10322020, ECO:0000269|PubMed:19542270}.
CC -!- ACTIVITY REGULATION: Is inhibited in vitro by para-
CC hydroxymercuribenzoate, a sulfydryl inhibitor.
CC {ECO:0000269|PubMed:10206711}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:10206711};
CC -!- SUBCELLULAR LOCATION: Secreted, cell wall {ECO:0000269|PubMed:10206711,
CC ECO:0000269|PubMed:14594841}. Note=LytF is localized at cell separation
CC sites and cell poles of rod-shaped cells during vegetative growth.
CC -!- INDUCTION: Expressed in the vegetative growth phase under exclusive
CC control of sigma-D (SigD). Expression of lytF is heterogeneous in the
CC exponentially growing cell population; it is ON in single cells and OFF
CC in long chains. The same subpopulation of cells that express lytF also
CC express flagellin. {ECO:0000269|PubMed:10206711,
CC ECO:0000269|PubMed:10322020, ECO:0000269|PubMed:19542270}.
CC -!- DOMAIN: The N-terminal domain contains LysM domains that are thought to
CC be involved in peptidoglycan binding, while the C-terminal domain is
CC endowed with the catalytic activity. {ECO:0000269|PubMed:10322020}.
CC -!- DISRUPTION PHENOTYPE: Cells from an undomesticated strain (3610)
CC lacking this gene grow predominantly as chains, whereas wild-type cells
CC grow as separate individuals. They do not show a reduction in the rate
CC of swarming motility. {ECO:0000269|PubMed:19542270}.
CC -!- SIMILARITY: Belongs to the peptidase C40 family. {ECO:0000255|PROSITE-
CC ProRule:PRU01284, ECO:0000305}.
CC -!- CAUTION: In domesticated laboratory strains (168 and derivatives), lytF
CC is not expressed in a majority of the growing cells. These cells form a
CC subpopulation that grows in multicellular, nonmotile chains.
CC Undomesticated strains (3610) express lytF in a majority of the
CC population, that grows as separate individual motile cells
CC (PubMed:19542270). {ECO:0000305|PubMed:19542270}.
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DR EMBL; Y14079; CAA74437.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB12776.2; -; Genomic_DNA.
DR PIR; B69825; B69825.
DR RefSeq; NP_388818.2; NC_000964.3.
DR RefSeq; WP_003244874.1; NZ_JNCM01000035.1.
DR AlphaFoldDB; O07532; -.
DR SMR; O07532; -.
DR STRING; 224308.BSU09370; -.
DR CAZy; CBM50; Carbohydrate-Binding Module Family 50.
DR MEROPS; C40.002; -.
DR PaxDb; O07532; -.
DR PRIDE; O07532; -.
DR EnsemblBacteria; CAB12776; CAB12776; BSU_09370.
DR GeneID; 939271; -.
DR KEGG; bsu:BSU09370; -.
DR PATRIC; fig|224308.179.peg.1010; -.
DR eggNOG; COG0791; Bacteria.
DR eggNOG; COG1388; Bacteria.
DR InParanoid; O07532; -.
DR OMA; TIYVNQV; -.
DR PhylomeDB; O07532; -.
DR BioCyc; BSUB:BSU09370-MON; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-KW.
DR GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0008932; F:lytic endotransglycosylase activity; IBA:GO_Central.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR CDD; cd00118; LysM; 5.
DR Gene3D; 3.10.350.10; -; 5.
DR InterPro; IPR018392; LysM_dom.
DR InterPro; IPR036779; LysM_dom_sf.
DR InterPro; IPR000064; NLP_P60_dom.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR Pfam; PF01476; LysM; 5.
DR Pfam; PF00877; NLPC_P60; 1.
DR SMART; SM00257; LysM; 5.
DR SUPFAM; SSF54001; SSF54001; 1.
DR SUPFAM; SSF54106; SSF54106; 5.
DR PROSITE; PS51782; LYSM; 5.
DR PROSITE; PS51935; NLPC_P60; 1.
PE 1: Evidence at protein level;
KW Cell wall; Cell wall biogenesis/degradation; Direct protein sequencing;
KW Hydrolase; Protease; Reference proteome; Repeat; Secreted; Signal;
KW Thiol protease.
FT SIGNAL 1..26
FT /evidence="ECO:0000269|PubMed:10206711"
FT CHAIN 27..488
FT /note="Peptidoglycan endopeptidase LytF"
FT /id="PRO_0000019753"
FT DOMAIN 27..70
FT /note="LysM 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT DOMAIN 92..135
FT /note="LysM 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT DOMAIN 174..217
FT /note="LysM 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT DOMAIN 240..283
FT /note="LysM 4"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT DOMAIN 307..350
FT /note="LysM 5"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01118"
FT DOMAIN 370..488
FT /note="NlpC/P60"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT REGION 70..93
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 137..176
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 218..239
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 286..306
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 400
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT ACT_SITE 449
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT ACT_SITE 461
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT CONFLICT 87
FT /note="K -> M (in Ref. 1; CAA74437)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 488 AA; 51395 MW; 4C2191EF2E059CB4 CRC64;
MKKKLAAGLT ASAIVGTTLV VTPAEAATIK VKSGDSLWKL AQTYNTSVAA LTSANHLSTT
VLSIGQTLTI PGSKSSTSSS TSSSTTKKSG SSVYTVKSGD SLWLIANEFK MTVQELKKLN
GLSSDLIRAG QKLKVSGTVS SSSSSSKKSN SNKSSSSSSK SSSNKSSSSS SSTGTYKVQL
GDSLWKIANK VNMSIAELKV LNNLKSDTIY VNQVLKTKSS GSDTSSKDNS SKSNQTSATT
KYTVKSGDSL WKIANNYNLT VQQIRNINNL KSDVLYVGQV LKLTGKASSG SSSSSSSSSN
ASSGTTTTYT VKSGDSLWVI AQKFNVTAQQ IREKNNLKTD VLQVGQKLVI SGKASSSSSS
GSSNTTSSTS AKINTMISAA KAQLGVPYRW GGTTPSGFDC SGFIYYVLNK VTSVSRLTAA
GYWNTMKSVS QPAVGDFVFF STYKAGPSHV GIYLGNGEFI NANDSGVVIS NMNNSYWKQR
YLGAKRYF
