YKFC_BACC1
ID YKFC_BACC1 Reviewed; 333 AA.
AC Q736M3;
DT 30-AUG-2017, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase {ECO:0000305};
DE EC=3.4.14.13 {ECO:0000250|UniProtKB:O35010};
DE AltName: Full=Gamma-D-glutamyl-L-diamino acid endopeptidase {ECO:0000303|PubMed:20944232};
DE Flags: Precursor;
GN Name=ykfC {ECO:0000303|PubMed:20944232};
GN OrderedLocusNames=BCE_2878 {ECO:0000312|EMBL:AAS41789.1};
OS Bacillus cereus (strain ATCC 10987 / NRS 248).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=222523;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 10987 / NRS 248;
RX PubMed=14960714; DOI=10.1093/nar/gkh258;
RA Rasko D.A., Ravel J., Oekstad O.A., Helgason E., Cer R.Z., Jiang L.,
RA Shores K.A., Fouts D.E., Tourasse N.J., Angiuoli S.V., Kolonay J.F.,
RA Nelson W.C., Kolstoe A.-B., Fraser C.M., Read T.D.;
RT "The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic
RT adaptations and a large plasmid related to Bacillus anthracis pXO1.";
RL Nucleic Acids Res. 32:977-988(2004).
RN [2] {ECO:0007744|PDB:3H41}
RP X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS) OF 24-333 IN COMPLEX WITH
RP L-ALA-GAMMA-D-GLU, SUBUNIT, AND ACTIVE SITE.
RC STRAIN=ATCC 10987 / NRS 248;
RX PubMed=20944232; DOI=10.1107/s1744309110021214;
RA Xu Q., Abdubek P., Astakhova T., Axelrod H.L., Bakolitsa C., Cai X.,
RA Carlton D., Chen C., Chiu H.J., Chiu M., Clayton T., Das D., Deller M.C.,
RA Duan L., Ellrott K., Farr C.L., Feuerhelm J., Grant J.C., Grzechnik A.,
RA Han G.W., Jaroszewski L., Jin K.K., Klock H.E., Knuth M.W., Kozbial P.,
RA Krishna S.S., Kumar A., Lam W.W., Marciano D., Miller M.D., Morse A.T.,
RA Nigoghossian E., Nopakun A., Okach L., Puckett C., Reyes R., Tien H.J.,
RA Trame C.B., van den Bedem H., Weekes D., Wooten T., Yeh A., Hodgson K.O.,
RA Wooley J., Elsliger M.A., Deacon A.M., Godzik A., Lesley S.A., Wilson I.A.;
RT "Structure of the gamma-D-glutamyl-L-diamino acid endopeptidase YkfC from
RT Bacillus cereus in complex with L-Ala-gamma-D-Glu: insights into substrate
RT recognition by NlpC/P60 cysteine peptidases.";
RL Acta Crystallogr. F 66:1354-1364(2010).
CC -!- FUNCTION: Specifically hydrolyzes gamma-D-glutamyl-L-lysine bonds in
CC murein peptides, releasing L-Ala-D-Glu. {ECO:0000250|UniProtKB:O35010}.
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:0000250|UniProtKB:O35010};
CC -!- PATHWAY: Cell wall degradation; peptidoglycan degradation.
CC {ECO:0000250|UniProtKB:O35010}.
CC -!- SUBUNIT: Monomer in solution. {ECO:0000269|PubMed:20944232}.
CC -!- SIMILARITY: Belongs to the peptidase C40 family. {ECO:0000255|PROSITE-
CC ProRule:PRU01284, ECO:0000305}.
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DR EMBL; AE017194; AAS41789.1; -; Genomic_DNA.
DR RefSeq; WP_000755410.1; NC_003909.8.
DR PDB; 3H41; X-ray; 1.79 A; A=23-333.
DR PDBsum; 3H41; -.
DR AlphaFoldDB; Q736M3; -.
DR SMR; Q736M3; -.
DR DNASU; 2750805; -.
DR EnsemblBacteria; AAS41789; AAS41789; BCE_2878.
DR GeneID; 59160065; -.
DR KEGG; bca:BCE_2878; -.
DR HOGENOM; CLU_016043_13_2_9; -.
DR OMA; YEEKLWL; -.
DR BRENDA; 3.4.14.13; 648.
DR UniPathway; UPA00549; -.
DR EvolutionaryTrace; Q736M3; -.
DR Proteomes; UP000002527; 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 InterPro; IPR041382; SH3_16.
DR Pfam; PF00877; NLPC_P60; 1.
DR Pfam; PF18348; SH3_16; 1.
DR SUPFAM; SSF54001; SSF54001; 1.
DR PROSITE; PS51935; NLPC_P60; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell wall biogenesis/degradation; Hydrolase; Protease;
KW Signal; Thiol protease.
FT SIGNAL 1..23
FT /evidence="ECO:0000255"
FT CHAIN 24..333
FT /note="Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase"
FT /id="PRO_5004285596"
FT DOMAIN 208..332
FT /note="NlpC/P60"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284"
FT ACT_SITE 238
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284,
FT ECO:0000305|PubMed:20944232"
FT ACT_SITE 291
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284,
FT ECO:0000305|PubMed:20944232"
FT ACT_SITE 303
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01284,
FT ECO:0000305|PubMed:20944232"
FT BINDING 83
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20944232"
FT BINDING 118
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20944232"
FT BINDING 237..239
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20944232"
FT BINDING 256..257
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:20944232"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 35..45
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 56..58
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 61..67
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 70..78
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 82..87
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 91..98
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:3H41"
FT TURN 136..138
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 146..155
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 169..175
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 177..183
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 211..219
FT /evidence="ECO:0007829|PDB:3H41"
FT TURN 220..223
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 238..247
FT /evidence="ECO:0007829|PDB:3H41"
FT TURN 248..250
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 257..260
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 263..267
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 269..271
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 277..281
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 282..285
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 289..297
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 300..303
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 309..317
FT /evidence="ECO:0007829|PDB:3H41"
FT HELIX 321..324
FT /evidence="ECO:0007829|PDB:3H41"
FT STRAND 325..330
FT /evidence="ECO:0007829|PDB:3H41"
SQ SEQUENCE 333 AA; 37274 MW; 5AFF15DB6816D742 CRC64;
MKKVGTAFLT TLFIFSSFTS AHAEEKKDSK AFIDVSAATL WTAPDSLRPI DVPSATNPVD
LWKWTKSMTL DEKLWLTNAN KLETQALLGQ EVTVVDKKGD WVKVLVHGQP TPRNEEGYPG
WMPEKQLTYN QEFADKTNEP FVLVTKPTAI LYINPSEKHK SLEVSYNTRL PLLSEDTISY
RVLLPNGQKA WLRKNDGTFY RSQNDIPTPA ADDLINTGKM FLGLPYIWAG TSGFGFDCSG
FTHTIYKSHG ITIPRDSGPQ SRNGVAVDKE HLQKGDLIFF AHDQGKGSVH HVAMYIGDGN
MIHSPRAERS VEIIPLNTPG YIEEYAGARR YLP
