ID B9YC96_9FIRM Unreviewed; 383 AA.
AC B9YC96;
DT 14-APR-2009, integrated into UniProtKB/TrEMBL.
DT 14-APR-2009, sequence version 1.
DT 24-JAN-2024, entry version 56.
DE RecName: Full=serine-type D-Ala-D-Ala carboxypeptidase {ECO:0000256|ARBA:ARBA00012448};
DE EC=3.4.16.4 {ECO:0000256|ARBA:ARBA00012448};
GN ORFNames=HOLDEFILI_03455 {ECO:0000313|EMBL:EEF66418.1};
OS Holdemania filiformis DSM 12042.
OC Bacteria; Bacillota; Erysipelotrichia; Erysipelotrichales;
OC Erysipelotrichaceae; Holdemania.
OX NCBI_TaxID=545696 {ECO:0000313|EMBL:EEF66418.1, ECO:0000313|Proteomes:UP000005950};
RN [1] {ECO:0000313|EMBL:EEF66418.1, ECO:0000313|Proteomes:UP000005950}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 12042 {ECO:0000313|EMBL:EEF66418.1,
RC ECO:0000313|Proteomes:UP000005950};
RA Fulton L., Clifton S., Fulton B., Xu J., Minx P., Pepin K.H., Johnson M.,
RA Bhonagiri V., Nash W.E., Mardis E.R., Wilson R.K.;
RL Submitted (DEC-2008) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:EEF66418.1, ECO:0000313|Proteomes:UP000005950}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 12042 {ECO:0000313|EMBL:EEF66418.1,
RC ECO:0000313|Proteomes:UP000005950};
RA Sudarsanam P., Ley R., Guruge J., Turnbaugh P.J., Mahowald M., Liep D.,
RA Gordon J.;
RT "Draft genome sequence of Holdemania filiformis DSM 12042.";
RL Submitted (FEB-2009) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Removes C-terminal D-alanyl residues from sugar-peptide cell
CC wall precursors. {ECO:0000256|ARBA:ARBA00003217}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Preferential cleavage: (Ac)2-L-Lys-D-Ala-|-D-Ala. Also
CC transpeptidation of peptidyl-alanyl moieties that are N-acyl
CC substituents of D-alanine.; EC=3.4.16.4;
CC Evidence={ECO:0000256|ARBA:ARBA00034000};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000256|ARBA:ARBA00004752}.
CC -!- SIMILARITY: Belongs to the peptidase S11 family.
CC {ECO:0000256|ARBA:ARBA00007164, ECO:0000256|RuleBase:RU004016}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EEF66418.1}.
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DR EMBL; ACCF01000217; EEF66418.1; -; Genomic_DNA.
DR RefSeq; WP_006060607.1; NZ_GG657561.1.
DR AlphaFoldDB; B9YC96; -.
DR STRING; 545696.HOLDEFILI_03455; -.
DR MEROPS; S11.005; -.
DR GeneID; 83016904; -.
DR eggNOG; COG1686; Bacteria.
DR HOGENOM; CLU_027070_8_0_9; -.
DR OrthoDB; 9791132at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000005950; Unassembled WGS sequence.
DR GO; GO:0009002; F:serine-type D-Ala-D-Ala carboxypeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 2.60.410.10; D-Ala-D-Ala carboxypeptidase, C-terminal domain; 1.
DR Gene3D; 3.40.710.10; DD-peptidase/beta-lactamase superfamily; 1.
DR InterPro; IPR012338; Beta-lactam/transpept-like.
DR InterPro; IPR015956; Peniciliin-bd_prot_C_sf.
DR InterPro; IPR018044; Peptidase_S11.
DR InterPro; IPR012907; Peptidase_S11_C.
DR InterPro; IPR037167; Peptidase_S11_C_sf.
DR InterPro; IPR001967; Peptidase_S11_N.
DR PANTHER; PTHR21581; D-ALANYL-D-ALANINE CARBOXYPEPTIDASE; 1.
DR PANTHER; PTHR21581:SF6; TRAFFICKING PROTEIN PARTICLE COMPLEX SUBUNIT 12; 1.
DR Pfam; PF07943; PBP5_C; 1.
DR Pfam; PF00768; Peptidase_S11; 1.
DR PRINTS; PR00725; DADACBPTASE1.
DR SMART; SM00936; PBP5_C; 1.
DR SUPFAM; SSF56601; beta-lactamase/transpeptidase-like; 1.
DR SUPFAM; SSF69189; Penicillin-binding protein associated domain; 1.
PE 3: Inferred from homology;
KW Carboxypeptidase {ECO:0000256|ARBA:ARBA00022645,
KW ECO:0000313|EMBL:EEF66418.1}; Cell shape {ECO:0000256|ARBA:ARBA00022960};
KW Cell wall biogenesis/degradation {ECO:0000256|ARBA:ARBA00023316};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Peptidoglycan synthesis {ECO:0000256|ARBA:ARBA00022984};
KW Protease {ECO:0000256|ARBA:ARBA00022670};
KW Signal {ECO:0000256|ARBA:ARBA00022729, ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..20
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 21..383
FT /note="serine-type D-Ala-D-Ala carboxypeptidase"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5039513678"
FT DOMAIN 277..367
FT /note="Peptidase S11 D-Ala-D-Ala carboxypeptidase A C-
FT terminal"
FT /evidence="ECO:0000259|SMART:SM00936"
FT ACT_SITE 59
FT /note="Acyl-ester intermediate"
FT /evidence="ECO:0000256|PIRSR:PIRSR618044-1"
FT ACT_SITE 62
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|PIRSR:PIRSR618044-1"
FT ACT_SITE 119
FT /evidence="ECO:0000256|PIRSR:PIRSR618044-1"
FT BINDING 227
FT /ligand="substrate"
FT /evidence="ECO:0000256|PIRSR:PIRSR618044-2"
SQ SEQUENCE 383 AA; 41795 MW; 30C7C75BF5979B0B CRC64;
MKKLASIVIA LSLFLVSVHA TTSQGVDLTP SAKAAILIDY ETGQILYEKN SSAKLYPASM
TKMMSLLLVV EAIHNGKLSW DTEVTASAHA SSMGGSQIFL ETGEVMTVED LYKASTVASA
NDAIVALAEK VGGSEENFAA MMNEKAEQLG LEQTHFVNAT GLHDDNHYSC AKDMAAIGRA
LIQEGQDDIL RFTSTYDDYI RADTENKFWL VNTNKLIRTY QGMDGLKTGY TTQSMYCITV
TAKRDGLRLI GVAMGEPTRD VRNSEASALL DYGFSTYGYQ IEMEKGTPVT TIKVDNGKPD
EVRLVTKEAI GHIVAKGAQS ALINTEIVLD KKKAPIQAGE TVGRVILHFE DGTQIGQDLV
AEEAIMPLDF IDILLKTWKK LLF
//