YKFC_BACSU
ID YKFC_BACSU Reviewed; 296 AA.
AC O35010; Q796M4;
DT 20-JAN-2009, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 2.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase {ECO:0000305};
DE EC=3.4.14.13 {ECO:0000269|PubMed:11747447};
DE AltName: Full=Cell wall endopeptidase YkfC {ECO:0000305};
GN Name=ykfC; OrderedLocusNames=BSU12990;
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 Devine K.M.;
RT "Sequence of the Bacillus subtilis genome between xlyA and ykoR.";
RL Submitted (NOV-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 TO 228.
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 FUNCTION AS AN ENDOPEPTIDASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND PROBABLE ROLE IN MUREIN PEPTIDE METABOLISM.
RC STRAIN=168;
RX PubMed=11747447; DOI=10.1021/bi011640x;
RA Schmidt D.M.Z., Hubbard B.K., Gerlt J.A.;
RT "Evolution of enzymatic activities in the enolase superfamily: functional
RT assignment of unknown proteins in Bacillus subtilis and Escherichia coli as
RT L-Ala-D/L-Glu epimerases.";
RL Biochemistry 40:15707-15715(2001).
RN [5]
RP INDUCTION.
RX PubMed=15101989; DOI=10.1111/j.1365-2958.2004.04023.x;
RA Hamon M.A., Stanley N.R., Britton R.A., Grossman A.D., Lazazzera B.A.;
RT "Identification of AbrB-regulated genes involved in biofilm formation by
RT Bacillus subtilis.";
RL Mol. Microbiol. 52:847-860(2004).
CC -!- FUNCTION: Specifically hydrolyzes gamma-D-glutamyl-L-lysine bonds in
CC murein peptides, releasing L-Ala-D-Glu. {ECO:0000269|PubMed:11747447}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=The enzyme releases L-Ala-gamma-D-Glu dipeptides from cell
CC wall peptides via cleavage of an L-Ala-gamma-D-Glu-|-L-Lys bond.;
CC EC=3.4.14.13; Evidence={ECO:0000269|PubMed:11747447};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=310 uM for L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala
CC {ECO:0000269|PubMed:11747447};
CC KM=120 uM for L-Ala-gamma-D-Glu-L-Lys-D-Ala
CC {ECO:0000269|PubMed:11747447};
CC KM=290 uM for L-Ala-gamma-D-Glu-L-Lys {ECO:0000269|PubMed:11747447};
CC Note=kcat is 5.7 sec(-1) with L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala as
CC substrate. kcat is 2.6 sec(-1) with L-Ala-gamma-D-Glu-L-Lys-D-Ala as
CC substrate. kcat is 1.2 sec(-1) with L-Ala-gamma-D-Glu-L-Lys as
CC substrate. {ECO:0000269|PubMed:11747447};
CC -!- PATHWAY: Cell wall degradation; peptidoglycan degradation.
CC {ECO:0000305|PubMed:11747447}.
CC -!- INDUCTION: Repressed by AbrB, a transcription factor that negatively
CC controls biofilm formation. {ECO:0000269|PubMed:15101989}.
CC -!- SIMILARITY: Belongs to the peptidase C40 family. {ECO:0000255|PROSITE-
CC ProRule:PRU01284, ECO:0000305}.
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DR EMBL; AJ002571; CAA05579.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB13156.2; -; Genomic_DNA.
DR PIR; A69856; A69856.
DR RefSeq; NP_389182.2; NC_000964.3.
DR RefSeq; WP_003245577.1; NZ_JNCM01000035.1.
DR AlphaFoldDB; O35010; -.
DR SMR; O35010; -.
DR STRING; 224308.BSU12990; -.
DR MEROPS; C40.009; -.
DR PaxDb; O35010; -.
DR PRIDE; O35010; -.
DR EnsemblBacteria; CAB13156; CAB13156; BSU_12990.
DR GeneID; 937979; -.
DR KEGG; bsu:BSU12990; -.
DR PATRIC; fig|224308.179.peg.1411; -.
DR eggNOG; COG0791; Bacteria.
DR InParanoid; O35010; -.
DR OMA; YEEKLWL; -.
DR PhylomeDB; O35010; -.
DR BioCyc; BSUB:BSU12990-MON; -.
DR BRENDA; 3.4.14.13; 658.
DR SABIO-RK; O35010; -.
DR UniPathway; UPA00549; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0008234; F:cysteine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0016998; P:cell wall macromolecule catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR InterPro; IPR000064; NLP_P60_dom.
DR InterPro; IPR038765; Papain-like_cys_pep_sf.
DR Pfam; PF00877; NLPC_P60; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS51935; NLPC_P60; 1.
PE 1: Evidence at protein level;
KW Cell wall biogenesis/degradation; Hydrolase; Protease; Reference proteome;
KW Thiol protease.
FT CHAIN 1..296
FT /note="Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase"
FT /id="PRO_0000360812"
FT DOMAIN 170..295
FT /note="NlpC/P60"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT ACT_SITE 200
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT ACT_SITE 253
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT ACT_SITE 265
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT BINDING 90
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q736M3"
FT BINDING 199..201
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q736M3"
FT BINDING 218..219
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q736M3"
FT CONFLICT 228
FT /note="G -> V (in Ref. 1; CAA05579)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 296 AA; 33025 MW; 6B1F0F4480D4FC1E CRC64;
MMHTVISAVA NIWTAPDSPR PSDQFMLQPT VMIRDWLERM TYDERLGLCT DNVIQTQVLF
GEKVLVTAEQ GEWVSVIVPS QPSRKDPRGY PGWMKKYQLE KTKPIHTQHD VMISKPAAFL
YRSNGEKEIE LSFLTVLPLI AKENGYFKVS TVFGERFVRQ SDAVPVSQQK GTAEDIIQTG
AFFLGLPYLW GGISGFGFDC SGFMYSIFKA NGYSIPRDAG DQAKAGKGVP LDDMKAGDLL
FFAYEEGKGA IHHVGLYVGG GKMLHSPKTG KSIEILTLTE TIYEKELCAV RRCFSE
