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Entry version 144 (02 Dec 2020)
Sequence version 1 (01 Oct 1994)
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Protein

D-alanyl-D-alanine carboxypeptidase DacD

Gene

dacD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score:

Annotation score:4 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>
-Protein inferred from homologyi <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%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

  • 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%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 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%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 sitei65Acyl-ester intermediateBy similarity1
Active sitei68Proton acceptorBy similarity1
Active sitei131By similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei234SubstrateBy 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

GO - Biological processi

<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

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%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:
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%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:dacD
Synonyms:phsE, phsF
Ordered Locus Names:STM2062
<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>OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
<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 identifieri99287 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
<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
  • UP000001014 <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

<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 – 23Sequence analysisAdd BLAST23
<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_000002723524 – 390D-alanyl-D-alanine carboxypeptidase DacDAdd BLAST367

Proteomic databases

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

More...
PaxDbi
P37604

<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

3D structure databases

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

More...
SMRi
P37604

Database of comparative protein structure models

More...
ModBasei
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

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_027070_8_1_6

Identification of Orthologs from Complete Genome Data

More...
OMAi
IQAGSWV

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P37604

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%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.

<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 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.

P37604-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLLKRRLFIA ASLFAMHLSP ALAADAVSFA PQPPAIDAGA WVLMDYTTGQ
60 70 80 90 100
VLTAGNEHQQ RNPASLTKLM TGYVVDRAID SHRISPDDIV TVGRDAWAKD
110 120 130 140 150
NPVFVGSSLM FLKEGDRVSV RDLSRGLIVD SGNDACVALA DYIAGGQPQF
160 170 180 190 200
VAMMNSYVKK LNLQDTHFET VHGLDAPGQH SSAYDLAVLS RAIIHGEPEF
210 220 230 240 250
YHMYSEKSLT WNGITQQNRN GLLWDKTMHI DGLKTGHTSG AGFNLIASAV
260 270 280 290 300
DGQRRLIAVV MGAKSSKGRE EQARKLLQWG QQNFATVQIL HSGKKVGSER
310 320 330 340 350
IWYGDKEKIA LGTEQDFWMA LPKAEIPHIK AKYVLDRKEL EAPIAAHQQV
360 370 380 390
GEIELYDRDK LIAQWPLVTL ESVGKGGMFS RLSDYFQHKA
Length:390
Mass (Da):43,097
Last modified:October 1, 1994 - 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:iE7BD51C17CE8F01B
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 AAA68435 differs from that shown. Reason: Frameshift.Curated
The sequence AAA68436 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
L31538 Genomic DNA Translation: AAA68435.1 Frameshift.
L31538 Genomic DNA Translation: AAA68436.1 Different initiation.
AE006468 Genomic DNA Translation: AAL20966.1
L32188 Genomic DNA Translation: AAC36937.1

Protein sequence database of the Protein Information Resource

More...
PIRi
D57143

NCBI Reference Sequences

More...
RefSeqi
NP_461007.1, NC_003197.2
WP_000925042.1, NC_003197.2

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAL20966; AAL20966; STM2062

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
1253583

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
stm:STM2062

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|99287.12.peg.2184

<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
L31538 Genomic DNA Translation: AAA68435.1 Frameshift.
L31538 Genomic DNA Translation: AAA68436.1 Different initiation.
AE006468 Genomic DNA Translation: AAL20966.1
L32188 Genomic DNA Translation: AAC36937.1
PIRiD57143
RefSeqiNP_461007.1, NC_003197.2
WP_000925042.1, NC_003197.2

3D structure databases

SMRiP37604
ModBaseiSearch...

Protein family/group databases

MEROPSiS11.009

Proteomic databases

PaxDbiP37604

Genome annotation databases

EnsemblBacteriaiAAL20966; AAL20966; STM2062
GeneIDi1253583
KEGGistm:STM2062
PATRICifig|99287.12.peg.2184

Phylogenomic databases

HOGENOMiCLU_027070_8_1_6
OMAiIQAGSWV
PhylomeDBiP37604

Enzyme and pathway databases

UniPathwayiUPA00219

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

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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_SALTY
<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: P37604
Secondary accession number(s): P37605
<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: October 1, 1994
Last sequence update: October 1, 1994
Last modified: December 2, 2020
This is version 144 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

Reference proteome

Documents

  1. Peptidase families
    Classification of peptidase families and list of entries
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families
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