LDCA_ECOLI
ID LDCA_ECOLI Reviewed; 304 AA.
AC P76008; O87499;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=Murein tetrapeptide carboxypeptidase;
DE EC=3.4.17.13;
DE AltName: Full=LD-carboxypeptidase A;
DE AltName: Full=Muramoyltetrapeptide carboxypeptidase;
GN Name=ldcA; Synonyms=ycgQ; OrderedLocusNames=b1192, JW1181;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION IN MUREIN RECYCLING, CATALYTIC
RP ACTIVITY, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION, PATHWAY, DISRUPTION
RP PHENOTYPE, AND SUBCELLULAR LOCATION.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=10428950; DOI=10.1093/emboj/18.15.4108;
RA Templin M.F., Ursinus A., Hoeltje J.-V.;
RT "A defect in cell wall recycling triggers autolysis during the stationary
RT growth phase of Escherichia coli.";
RL EMBO J. 18:4108-4117(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION IN PEPTIDOGLYCAN RECYCLING, AND REVIEW.
RX PubMed=18535144; DOI=10.1128/mmbr.00027-07;
RA Park J.T., Uehara T.;
RT "How bacteria consume their own exoskeletons (turnover and recycling of
RT cell wall peptidoglycan).";
RL Microbiol. Mol. Biol. Rev. 72:211-227(2008).
CC -!- FUNCTION: Releases the terminal D-alanine residue from the cytoplasmic
CC tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a
CC lesser extent, can also cleave D-Ala from murein derivatives containing
CC the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide,
CC GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not
CC act on murein sacculi or cross-linked muropeptides. The tripeptides
CC produced by the LcdA reaction can then be reused as peptidoglycan
CC building blocks; LcdA is thereby involved in murein recycling. Is also
CC essential for viability during stationary phase.
CC {ECO:0000269|PubMed:10428950, ECO:0000269|PubMed:18535144}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-acetyl-D-glucosaminyl-N-acetylmuramoyl-L-alanyl-D-
CC glutamyl-6-carboxy-L-lysyl-D-alanine = D-alanine + N-acetyl-D-
CC glucosaminyl-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl;
CC Xref=Rhea:RHEA:48688, ChEBI:CHEBI:15377, ChEBI:CHEBI:57416,
CC ChEBI:CHEBI:90762, ChEBI:CHEBI:90763; EC=3.4.17.13;
CC Evidence={ECO:0000269|PubMed:10428950};
CC -!- ACTIVITY REGULATION: Inhibited by beta-lactams containing a D-amino
CC acid side chain. {ECO:0000269|PubMed:10428950}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan recycling.
CC {ECO:0000269|PubMed:10428950}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10428950}.
CC -!- DISRUPTION PHENOTYPE: Bacteriolysis during the stationary growth phase.
CC Cells lacking this gene also accumulate UDP-MurNAc-tetrapeptide, an
CC unusual compound that normally is not present at significant levels in
CC E.coli cells. {ECO:0000269|PubMed:10428950}.
CC -!- SIMILARITY: Belongs to the peptidase S66 family. {ECO:0000305}.
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DR EMBL; U00096; AAC74276.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA36050.1; -; Genomic_DNA.
DR PIR; E64865; E64865.
DR RefSeq; NP_415710.1; NC_000913.3.
DR RefSeq; WP_000051560.1; NZ_SSZK01000010.1.
DR PDB; 5Z01; X-ray; 1.75 A; A=1-304.
DR PDB; 5Z03; X-ray; 1.75 A; A/B=1-304.
DR PDBsum; 5Z01; -.
DR PDBsum; 5Z03; -.
DR AlphaFoldDB; P76008; -.
DR SMR; P76008; -.
DR BioGRID; 4259643; 325.
DR BioGRID; 850123; 1.
DR DIP; DIP-10085N; -.
DR IntAct; P76008; 4.
DR STRING; 511145.b1192; -.
DR MEROPS; S66.002; -.
DR jPOST; P76008; -.
DR PaxDb; P76008; -.
DR PRIDE; P76008; -.
DR EnsemblBacteria; AAC74276; AAC74276; b1192.
DR EnsemblBacteria; BAA36050; BAA36050; BAA36050.
DR GeneID; 945756; -.
DR KEGG; ecj:JW1181; -.
DR KEGG; eco:b1192; -.
DR PATRIC; fig|1411691.4.peg.1094; -.
DR EchoBASE; EB3657; -.
DR eggNOG; COG1619; Bacteria.
DR HOGENOM; CLU_034346_0_1_6; -.
DR InParanoid; P76008; -.
DR OMA; MLTQWRL; -.
DR PhylomeDB; P76008; -.
DR BioCyc; EcoCyc:G6621-MON; -.
DR BioCyc; MetaCyc:G6621-MON; -.
DR UniPathway; UPA00544; -.
DR PRO; PR:P76008; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0004180; F:carboxypeptidase activity; IDA:EcoCyc.
DR GO; GO:0106415; F:muramoyltetrapeptide carboxypeptidase activity; IEA:UniProtKB-EC.
DR GO; GO:0008236; F:serine-type peptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009050; P:glycopeptide catabolic process; IDA:EcoCyc.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009254; P:peptidoglycan turnover; 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; 3.40.50.10740; -; 1.
DR Gene3D; 3.50.30.60; -; 1.
DR InterPro; IPR027461; Carboxypeptidase_A_C_sf.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR027478; LdcA_N.
DR InterPro; IPR040449; Peptidase_S66_N.
DR InterPro; IPR040921; Peptidase_S66C.
DR InterPro; IPR003507; S66_fam.
DR PANTHER; PTHR30237; PTHR30237; 1.
DR Pfam; PF02016; Peptidase_S66; 1.
DR Pfam; PF17676; Peptidase_S66C; 1.
DR PIRSF; PIRSF028757; LD-carboxypeptidase; 1.
DR SUPFAM; SSF141986; SSF141986; 1.
DR SUPFAM; SSF52317; SSF52317; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carboxypeptidase; Cell shape;
KW Cell wall biogenesis/degradation; Cytoplasm; Hydrolase;
KW Peptidoglycan synthesis; Protease; Reference proteome; Serine protease.
FT CHAIN 1..304
FT /note="Murein tetrapeptide carboxypeptidase"
FT /id="PRO_0000172837"
FT ACT_SITE 106
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 200
FT /note="Charge relay system"
FT /evidence="ECO:0000250"
FT ACT_SITE 270
FT /note="Charge relay system"
FT /evidence="ECO:0000250"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 16..28
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 36..39
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 50..58
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 79..82
FT /evidence="ECO:0007829|PDB:5Z01"
FT TURN 83..85
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 88..95
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 101..104
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 106..108
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 109..119
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 123..125
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 129..133
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 140..151
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 153..159
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 166..176
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 177..181
FT /evidence="ECO:0007829|PDB:5Z01"
FT TURN 182..185
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 196..203
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 206..218
FT /evidence="ECO:0007829|PDB:5Z01"
FT TURN 219..221
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 222..224
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 225..235
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:5Z01"
FT HELIX 247..255
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 262..264
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 269..272
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 277..279
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 281..288
FT /evidence="ECO:0007829|PDB:5Z01"
FT STRAND 291..297
FT /evidence="ECO:0007829|PDB:5Z01"
SQ SEQUENCE 304 AA; 33567 MW; BD801CA75E2AC25F CRC64;
MSLFHLIAPS GYCIKQHAAL RGIQRLTDAG HQVNNVEVIA RRCERFAGTE TERLEDLNSL
ARLTTPNTIV LAVRGGYGAS RLLADIDWQA LVARQQHDPL LICGHSDFTA IQCGLLAHGN
VITFSGPMLV ANFGADELNA FTEHHFWLAL RNETFTIEWQ GEGPTCRAEG TLWGGNLAML
ISLIGTPWMP KIENGILVLE DINEHPFRVE RMLLQLYHAG ILPRQKAIIL GSFSGSTPND
YDAGYNLESV YAFLRSRLSI PLITGLDFGH EQRTVTLPLG AHAILNNTRE GTQLTISGHP
VLKM
