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UniProtKB - P76008 (LDCA_ECOLI)

Entry version 151 (02 Jun 2021)
Sequence version 1 (01 Feb 1997)
Previous versions | rss
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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei106NucleophileBy similarity1
Active sitei200Charge relay systemBy similarity1
Active sitei270Charge relay systemBy similarity1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

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 on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionCarboxypeptidase, Hydrolase, Protease, Serine protease
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:G6621-MONOMER
MetaCyc:G6621-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...UniPathwayi		UPA00544

Protein family/group databases

MEROPS protease database

More...MEROPSi		S66.002

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Murein tetrapeptide carboxypeptidase (EC:3.4.17.13)
Alternative name(s):
LD-carboxypeptidase A
Muramoyltetrapeptide carboxypeptidase
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ldcA
Synonyms:ycgQ
Ordered Locus Names:b1192, JW1181
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Cytoplasm

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>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

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001728371 – 304Murein tetrapeptide carboxypeptidaseAdd BLAST304

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P76008

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P76008

PRoteomics IDEntifications database

More...PRIDEi		P76008

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4259643, 325 interactors
850123, 1 interactor

Database of interacting proteins

More...DIPi		DIP-10085N

Protein interaction database and analysis system

More...IntActi		P76008, 4 interactors

STRING: functional protein association networks

More...STRINGi		511145.b1192

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1304
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P76008

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the peptidase S66 family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1619, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_034346_0_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P76008

Database for complete collections of gene phylogenies

More...PhylomeDBi		P76008

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.40.50.10740, 1 hit
3.50.30.60, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR027461, Carboxypeptidase_A_C_sf
IPR029062, Class_I_gatase-like
IPR027478, LdcA_N
IPR040449, Peptidase_S66_N
IPR040921, Peptidase_S66C
IPR003507, S66_fam

The PANTHER Classification System

More...PANTHERi		PTHR30237, PTHR30237, 1 hit

Pfam protein domain database

More...Pfami		View protein in Pfam
PF02016, Peptidase_S66, 1 hit
PF17676, Peptidase_S66C, 1 hit

PIRSF; a whole-protein classification database

More...PIRSFi		PIRSF028757, LD-carboxypeptidase, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF141986, SSF141986, 1 hit
SSF52317, SSF52317, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iBD801CA75E2AC25F
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74276.1
AP009048 Genomic DNA Translation: BAA36050.1

Protein sequence database of the Protein Information Resource

More...PIRi		E64865

NCBI Reference Sequences

More...RefSeqi		NP_415710.1, NC_000913.3
WP_000051560.1, NZ_SSZK01000010.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC74276; AAC74276; b1192
BAA36050; BAA36050; BAA36050

Database of genes from NCBI RefSeq genomes

More...GeneIDi		945756

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW1181
eco:b1192

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.1094

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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_SSZK01000010.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5Z01X-ray1.75A1-304[»]
5Z03X-ray1.75A/B1-304[»]
SMRiP76008
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4259643, 325 interactors
850123, 1 interactor
DIPiDIP-10085N
IntActiP76008, 4 interactors
STRINGi511145.b1192

Protein family/group databases

MEROPSiS66.002

Proteomic databases

jPOSTiP76008
PaxDbiP76008
PRIDEiP76008

Genome annotation databases

EnsemblBacteriaiAAC74276; AAC74276; b1192
BAA36050; BAA36050; BAA36050
GeneIDi945756
KEGGiecj:JW1181
eco:b1192
PATRICifig|1411691.4.peg.1094

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB3657

Phylogenomic databases

eggNOGiCOG1619, Bacteria
HOGENOMiCLU_034346_0_1_6
InParanoidiP76008
PhylomeDBiP76008

Enzyme and pathway databases

UniPathwayiUPA00544
BioCyciEcoCyc:G6621-MONOMER
MetaCyc:G6621-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P76008

Family and domain databases

Gene3Di3.40.50.10740, 1 hit
3.50.30.60, 1 hit
InterProiView protein in InterPro
IPR027461, Carboxypeptidase_A_C_sf
IPR029062, Class_I_gatase-like
IPR027478, LdcA_N
IPR040449, Peptidase_S66_N
IPR040921, Peptidase_S66C
IPR003507, S66_fam
PANTHERiPTHR30237, PTHR30237, 1 hit
PfamiView protein in Pfam
PF02016, Peptidase_S66, 1 hit
PF17676, Peptidase_S66C, 1 hit
PIRSFiPIRSF028757, LD-carboxypeptidase, 1 hit
SUPFAMiSSF141986, SSF141986, 1 hit
SSF52317, SSF52317, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiLDCA_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P76008
Secondary accession number(s): O87499
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: February 1, 1997
Last modified: June 2, 2021
This is version 151 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  5. SIMILARITY comments
    Index of protein domains and families
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