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UniProtKB - P33013 (DACD_ECOLI)

Entry version 167 (02 Jun 2021)
Sequence version 3 (15 Jul 1998)
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Protein

D-alanyl-D-alanine carboxypeptidase DacD

Gene

dacD

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

Removes C-terminal D-alanyl residues from sugar-peptide cell wall precursors.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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

  • Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine. EC:3.4.16.4

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan biosynthesis

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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 sitei63Acyl-ester intermediateBy similarity1
Active sitei66Proton acceptorBy similarity1
Active sitei129By similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei232SubstrateBy 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

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
Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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

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

More...UniPathwayi		UPA00219

Protein family/group databases

MEROPS protease database

More...MEROPSi		S11.009

<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_and_taxonomy_section">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:
D-alanyl-D-alanine carboxypeptidase DacD (EC:3.4.16.4)
Short name:
DD-carboxypeptidase
Short name:
DD-peptidase
Alternative name(s):
Penicillin-binding protein 6b
Short name:
PBP-6b
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:dacD
Synonyms:phsE, yeeC
Ordered Locus Names:b2010, JW5329
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_and_taxonomy_section">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_and_taxonomy_section">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_and_taxonomy_section">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_manual">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

Cell inner membrane, Cell membrane, Membrane

<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 denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 21Sequence analysisAdd BLAST21
<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_000002723422 – 388D-alanyl-D-alanine carboxypeptidase DacDAdd BLAST367

Proteomic databases

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

More...PaxDbi		P33013

PRoteomics IDEntifications database

More...PRIDEi		P33013

<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		4260413, 266 interactors

STRING: functional protein association networks

More...STRINGi		511145.b2010

<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

1388
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		P33013

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 S11 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1686, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_027070_8_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P33013

Database for complete collections of gene phylogenies

More...PhylomeDBi		P33013

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		2.60.410.10, 1 hit
3.40.710.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR012338, Beta-lactam/transpept-like
IPR015956, Peniciliin-bd_prot_C_sf
IPR018044, Peptidase_S11
IPR012907, Peptidase_S11_C
IPR037167, Peptidase_S11_C_sf
IPR001967, Peptidase_S11_N

Pfam protein domain database

More...Pfami		View protein in Pfam
PF07943, PBP5_C, 1 hit
PF00768, Peptidase_S11, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR00725, DADACBPTASE1

Simple Modular Architecture Research Tool; a protein domain database

More...SMARTi		View protein in SMART
SM00936, PBP5_C, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF56601, SSF56601, 1 hit
SSF69189, SSF69189, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P33013-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKRRLIIAAS LFVFNLSSGF AAENIPFSPQ PPEIHAGSWV LMDYTTGQIL 
        60         70         80         90        100
TAGNEHQQRN PASLTKLMTG YVVDRAIDSH RITPDDIVTV GRDAWAKDNP 
       110        120        130        140        150
VFVGSSLMFL KEGDRVSVRD LSRGLIVDSG NDACVALADY IAGGQRQFVE 
       160        170        180        190        200
MMNNYAEKLH LKDTHFETVH GLDAPGQHSS AYDLAVLSRA IIHGEPEFYH 
       210        220        230        240        250
MYSEKSLTWN GITQQNRNGL LWDKTMNVDG LKTGHTSGAG FNLIASAVDG 
       260        270        280        290        300
QRRLIAVVMG ADSAKGREEE ARKLLRWGQQ NFTTVQILHR GKKVGTERIW 
       310        320        330        340        350
YGDKENIDLG TEQEFWMVLP KAEIPHIKAK YTLDGKELTA PISAHQRVGE 
       360        370        380 
IELYDRDKQV AHWPLVTLES VGEGSMFSRL SDYFHHKA
Length:388
Mass (Da):43,346
Last modified:July 15, 1998 - v3
<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:i453FE18C21D207D0
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence AAA16416 differs from that shown. Reason: Erroneous initiation. Truncated N-terminus.Curated

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
U00009 Genomic DNA Translation: AAA16416.1 Different initiation.
U00096 Genomic DNA Translation: AAC75071.2
AP009048 Genomic DNA Translation: BAA15838.2

Protein sequence database of the Protein Information Resource

More...PIRi		A64966

NCBI Reference Sequences

More...RefSeqi		NP_416514.4, NC_000913.3
WP_000830156.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75071; AAC75071; b2010
BAA15838; BAA15838; BAA15838

Database of genes from NCBI RefSeq genomes

More...GeneIDi		946518

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW5329
eco:b2010

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.242

<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
U00009 Genomic DNA Translation: AAA16416.1 Different initiation.
U00096 Genomic DNA Translation: AAC75071.2
AP009048 Genomic DNA Translation: BAA15838.2
PIRiA64966
RefSeqiNP_416514.4, NC_000913.3
WP_000830156.1, NZ_LN832404.1

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
5FSRX-ray2.40A/B22-374[»]
SMRiP33013
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4260413, 266 interactors
STRINGi511145.b2010

Protein family/group databases

MEROPSiS11.009

Proteomic databases

PaxDbiP33013
PRIDEiP33013

Genome annotation databases

EnsemblBacteriaiAAC75071; AAC75071; b2010
BAA15838; BAA15838; BAA15838
GeneIDi946518
KEGGiecj:JW5329
eco:b2010
PATRICifig|1411691.4.peg.242

Organism-specific databases

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

More...EchoBASEi		EB1839

Phylogenomic databases

eggNOGiCOG1686, Bacteria
HOGENOMiCLU_027070_8_1_6
InParanoidiP33013
PhylomeDBiP33013

Enzyme and pathway databases

UniPathwayiUPA00219
BioCyciEcoCyc:RPOA-MONOMER
MetaCyc:RPOA-MONOMER

Miscellaneous databases

Protein Ontology

More...PROi		PR:P33013

Family and domain databases

Gene3Di2.60.410.10, 1 hit
3.40.710.10, 1 hit
InterProiView protein in InterPro
IPR012338, Beta-lactam/transpept-like
IPR015956, Peniciliin-bd_prot_C_sf
IPR018044, Peptidase_S11
IPR012907, Peptidase_S11_C
IPR037167, Peptidase_S11_C_sf
IPR001967, Peptidase_S11_N
PfamiView protein in Pfam
PF07943, PBP5_C, 1 hit
PF00768, Peptidase_S11, 1 hit
PRINTSiPR00725, DADACBPTASE1
SMARTiView protein in SMART
SM00936, PBP5_C, 1 hit
SUPFAMiSSF56601, SSF56601, 1 hit
SSF69189, SSF69189, 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 nameiDACD_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: P33013
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: July 15, 1998
Last modified: June 2, 2021
This is version 167 of the entry and version 3 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. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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