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Protein

Murein tetrapeptide carboxypeptidase

Gene

ldcA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Releases the terminal D-alanine residue from the cytoplasmic tetrapeptide recycling product L-Ala-gamma-D-Glu-meso-Dap-D-Ala. To a lesser extent, can also cleave D-Ala from murein derivatives containing the tetrapeptide, i.e. MurNAc-tetrapeptide, UDP-MurNAc-tetrapeptide, GlcNAc-MurNAc-tetrapeptide, and GlcNAc-anhMurNAc-tetrapeptide. Does not act on murein sacculi or cross-linked muropeptides. The tripeptides produced by the LcdA reaction can then be reused as peptidoglycan building blocks; LcdA is thereby involved in murein recycling. Is also essential for viability during stationary phase.2 Publications

Catalytic activityi

GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelyl-D-alanine + H2O = GlcNAc-MurNAc-L-alanyl-gamma-D-glutamyl-meso-diaminopimelate + D-alanine.1 Publication

Enzyme regulationi

Inhibited by beta-lactams containing a D-amino acid side chain.1 Publication

Pathwayi: peptidoglycan recycling

This protein is involved in the pathway peptidoglycan recycling, which is part of Cell wall biogenesis.1 Publication
View all proteins of this organism that are known to be involved in the pathway peptidoglycan recycling and in Cell wall biogenesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei106 – 1061NucleophileBy similarity
Active sitei200 – 2001Charge relay systemBy similarity
Active sitei270 – 2701Charge relay systemBy similarity

GO - Molecular functioni

  • carboxypeptidase activity Source: EcoCyc
  • serine-type peptidase activity Source: UniProtKB-KW

GO - Biological processi

  • cell wall organization Source: UniProtKB-KW
  • glycopeptide catabolic process Source: EcoCyc
  • peptidoglycan biosynthetic process Source: UniProtKB-KW
  • peptidoglycan turnover Source: EcoCyc
  • regulation of cell shape Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Carboxypeptidase, Hydrolase, Protease, Serine protease

Keywords - Biological processi

Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

BioCyciEcoCyc:G6621-MONOMER.
ECOL316407:JW1181-MONOMER.
MetaCyc:G6621-MONOMER.
UniPathwayiUPA00544.

Protein family/group databases

MEROPSiS66.002.

Names & Taxonomyi

Protein namesi
Recommended name:
Murein tetrapeptide carboxypeptidase (EC:3.4.17.13)
Alternative name(s):
LD-carboxypeptidase A
Muramoyltetrapeptide carboxypeptidase
Gene namesi
Name:ldcA
Synonyms:ycgQ
Ordered Locus Names:b1192, JW1181
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13898. ldcA.

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Bacteriolysis during the stationary growth phase. Cells lacking this gene also accumulate UDP-MurNAc-tetrapeptide, an unusual compound that normally is not present at significant levels in E.coli cells.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 304304Murein tetrapeptide carboxypeptidasePRO_0000172837Add
BLAST

Proteomic databases

PaxDbiP76008.

Interactioni

Protein-protein interaction databases

BioGridi4259643. 325 interactions.
DIPiDIP-10085N.
IntActiP76008. 4 interactions.
STRINGi511145.b1192.

Structurei

3D structure databases

ProteinModelPortaliP76008.
SMRiP76008. Positions 6-289.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase S66 family.Curated

Phylogenomic databases

eggNOGiENOG4105EBE. Bacteria.
COG1619. LUCA.
HOGENOMiHOG000025480.
InParanoidiP76008.
KOiK01297.
OMAiIVGHSDF.
PhylomeDBiP76008.

Family and domain databases

Gene3Di3.40.50.10740. 1 hit.
3.50.30.60. 1 hit.
InterProiIPR027461. Carboxypeptidase_A_C.
IPR029062. Class_I_gatase-like.
IPR027478. LdcA_N_dom.
IPR003507. S66_fam.
[Graphical view]
PfamiPF02016. Peptidase_S66. 1 hit.
[Graphical view]
PIRSFiPIRSF028757. LD-carboxypeptidase. 1 hit.
SUPFAMiSSF141986. SSF141986. 1 hit.
SSF52317. SSF52317. 1 hit.

Sequencei

Sequence statusi: Complete.

P76008-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLFHLIAPS GYCIKQHAAL RGIQRLTDAG HQVNNVEVIA RRCERFAGTE
60 70 80 90 100
TERLEDLNSL ARLTTPNTIV LAVRGGYGAS RLLADIDWQA LVARQQHDPL
110 120 130 140 150
LICGHSDFTA IQCGLLAHGN VITFSGPMLV ANFGADELNA FTEHHFWLAL
160 170 180 190 200
RNETFTIEWQ GEGPTCRAEG TLWGGNLAML ISLIGTPWMP KIENGILVLE
210 220 230 240 250
DINEHPFRVE RMLLQLYHAG ILPRQKAIIL GSFSGSTPND YDAGYNLESV
260 270 280 290 300
YAFLRSRLSI PLITGLDFGH EQRTVTLPLG AHAILNNTRE GTQLTISGHP

VLKM
Length:304
Mass (Da):33,567
Last modified:February 1, 1997 - v1
Checksum:iBD801CA75E2AC25F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74276.1.
AP009048 Genomic DNA. Translation: BAA36050.1.
PIRiE64865.
RefSeqiNP_415710.1. NC_000913.3.
WP_000051560.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74276; AAC74276; b1192.
BAA36050; BAA36050; BAA36050.
GeneIDi945756.
KEGGiecj:JW1181.
eco:b1192.
PATRICi32117632. VBIEscCol129921_1238.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74276.1.
AP009048 Genomic DNA. Translation: BAA36050.1.
PIRiE64865.
RefSeqiNP_415710.1. NC_000913.3.
WP_000051560.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP76008.
SMRiP76008. Positions 6-289.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259643. 325 interactions.
DIPiDIP-10085N.
IntActiP76008. 4 interactions.
STRINGi511145.b1192.

Protein family/group databases

MEROPSiS66.002.

Proteomic databases

PaxDbiP76008.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74276; AAC74276; b1192.
BAA36050; BAA36050; BAA36050.
GeneIDi945756.
KEGGiecj:JW1181.
eco:b1192.
PATRICi32117632. VBIEscCol129921_1238.

Organism-specific databases

EchoBASEiEB3657.
EcoGeneiEG13898. ldcA.

Phylogenomic databases

eggNOGiENOG4105EBE. Bacteria.
COG1619. LUCA.
HOGENOMiHOG000025480.
InParanoidiP76008.
KOiK01297.
OMAiIVGHSDF.
PhylomeDBiP76008.

Enzyme and pathway databases

UniPathwayiUPA00544.
BioCyciEcoCyc:G6621-MONOMER.
ECOL316407:JW1181-MONOMER.
MetaCyc:G6621-MONOMER.

Miscellaneous databases

PROiP76008.

Family and domain databases

Gene3Di3.40.50.10740. 1 hit.
3.50.30.60. 1 hit.
InterProiIPR027461. Carboxypeptidase_A_C.
IPR029062. Class_I_gatase-like.
IPR027478. LdcA_N_dom.
IPR003507. S66_fam.
[Graphical view]
PfamiPF02016. Peptidase_S66. 1 hit.
[Graphical view]
PIRSFiPIRSF028757. LD-carboxypeptidase. 1 hit.
SUPFAMiSSF141986. SSF141986. 1 hit.
SSF52317. SSF52317. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLDCA_ECOLI
AccessioniPrimary (citable) accession number: P76008
Secondary accession number(s): O87499
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: February 1, 1997
Last modified: September 7, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families
  5. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.