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Entry version 97 (29 Sep 2021)
Sequence version 1 (01 Jan 1998)
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Protein

Peptidoglycan deacetylase

Gene

pgdA

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
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

Catalyzes the N-deacetylation of peptidoglycan (PG), an important mechanism that appears to confer lysozyme resistance and to mitigate host immune detection; this likely contributes to pathogen persistence in the host. The exact nature of the residue in PG that is deacetylated has not been determined. Is also able to catalyze the deacetylation of acetylated xylan, and, to a lesser extent, that of chitin and chitosan. Therefore, this enzyme might play a role during infection, considering that xylan-containing carbohydrate structures are among those commonly consumed by humans.

4 Publications

<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

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

kcat is 775 min(-1), 968 min(-1), 2549 min(-1) and 1029 min(-1) with chitin, chitosan, acetylated xylan, and pNP-acetate as substrate, respectively.
  1. KM=0.85 mM for chitin1 Publication
  2. KM=0.85 mM for chitosan1 Publication
  3. KM=0.42 mM for acetylated xylan1 Publication
  4. KM=0.18 mM for pNP-acetate1 Publication

pH dependencei

Optimum pH is 6.0 with acetylated xylan as substrate. Is active at acidic pH ranging from 5.0 to 6.0.1 Publication

Temperature dependencei

Optimum temperature is 50 degrees Celsius with acetylated xylan as substrate. Retains about 80% of the activity at 30-55 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi14ZincBy similarity1
Metal bindingi86Zinc; via tele nitrogenBy similarity1
Metal bindingi90Zinc; via tele nitrogenBy 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 functionHydrolase
Biological processCarbohydrate metabolism, Cell wall biogenesis/degradation, Polysaccharide degradation, Stress response, Xylan degradation
LigandMetal-binding, Zinc

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

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BioCyci
HPY:HP0310-MONOMER

BRENDA Comprehensive Enzyme Information System

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BRENDAi
3.5.1.104, 2604

SABIO-RK: Biochemical Reaction Kinetics Database

More...
SABIO-RKi
O25080

<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:
Peptidoglycan deacetylase (EC:3.5.1.-)
Short name:
PG deacetylase
Alternative name(s):
Acetylxylan esterase (EC:3.1.1.72)
<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:pgdA
Ordered Locus Names:HP_0310, C694_01565
<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>OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
<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 identifieri85962 [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 lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
<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
  • UP000000429 <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

<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

Cells lacking this gene are considerably less resistant to lysozyme than wild-type, and show an absence or significantly reduced amount of N-deacetylated muropeptides in the bacterial PG. Mutant strains also have attenuated ability to colonize mouse stomachs, and induce a stronger immune response in the host. Disruption of this gene does not affect oxidative stress resistance characteristics, indicating that the major physiological role of the enzyme is not in combating oxidative stress.3 Publications

<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 <a href="http://www.uniprot.org/help/ptm_processing_section">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved1 Publication
<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_00004244382 – 293Peptidoglycan deacetylaseAdd BLAST292

Proteomic databases

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

More...
PaxDbi
O25080

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Its expression is markedly up-regulated upon cell exposure to oxidative stress. Is also significantly induced (3.5-fold) when H.pylori cells are in contact with macrophages.2 Publications

<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

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotetramer.

By similarity

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
85962.C694_01565

<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

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SMRi
O25080

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini29 – 276NodB homologyPROSITE-ProRule annotationAdd BLAST248

<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 polysaccharide deacetylase family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG0726, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_029940_1_0_7

Identification of Orthologs from Complete Genome Data

More...
OMAi
HNDFTPY

Database for complete collections of gene phylogenies

More...
PhylomeDBi
O25080

Family and domain databases

Conserved Domains Database

More...
CDDi
cd10938, CE4_HpPgdA_like, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR011330, Glyco_hydro/deAcase_b/a-brl
IPR002509, NODB_dom
IPR037950, PgdA-like

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01522, Polysacc_deac_1, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF88713, SSF88713, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS51677, NODB, 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.

O25080-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAKEILVAYG VDIDAVAGWL GSYGGEDSPD DISRGLFAGE VGIPRLLKLF
60 70 80 90 100
KKYHLPATWF SPGHSIETFS EQMKMIVDAG HEVGAHGYSH ENPIAMTAKQ
110 120 130 140 150
EEDVLLKSVE LIKDLTGKAP TGYVAPWWEF SNITNELLLK HGFKYDHSLM
160 170 180 190 200
HNDFTPYYVR VGDSWSKIDY SLEAKDWMKP LIRGVETDLV EIPANWYLDD
210 220 230 240 250
LPPMMFIKKS PNSFGFVSPH DIGQMWIDQF DWVYREMDYA VFSMTIHPDV
260 270 280 290
SARPQVLLMH EKIIEHINKH EGVRWVTFNE IADDFLKRNP RKK
Length:293
Mass (Da):33,677
Last modified:January 1, 1998 - 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:i42ADF39EE681532D
GO

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
AE000511 Genomic DNA Translation: AAD07376.1
CP003904 Genomic DNA Translation: AFV41534.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F64558

NCBI Reference Sequences

More...
RefSeqi
NP_207108.1, NC_000915.1
WP_001040419.1, NC_018939.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAD07376; AAD07376; HP_0310

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
heo:C694_01565
hpy:HP0310

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|85962.47.peg.330

<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
AE000511 Genomic DNA Translation: AAD07376.1
CP003904 Genomic DNA Translation: AFV41534.1
PIRiF64558
RefSeqiNP_207108.1, NC_000915.1
WP_001040419.1, NC_018939.1

3D structure databases

SMRiO25080
ModBaseiSearch...

Protein-protein interaction databases

STRINGi85962.C694_01565

Proteomic databases

PaxDbiO25080

Protocols and materials databases

The DNASU plasmid repository

More...
DNASUi
899203

Genome annotation databases

EnsemblBacteriaiAAD07376; AAD07376; HP_0310
KEGGiheo:C694_01565
hpy:HP0310
PATRICifig|85962.47.peg.330

Phylogenomic databases

eggNOGiCOG0726, Bacteria
HOGENOMiCLU_029940_1_0_7
OMAiHNDFTPY
PhylomeDBiO25080

Enzyme and pathway databases

BioCyciHPY:HP0310-MONOMER
BRENDAi3.5.1.104, 2604
SABIO-RKiO25080

Family and domain databases

CDDicd10938, CE4_HpPgdA_like, 1 hit
InterProiView protein in InterPro
IPR011330, Glyco_hydro/deAcase_b/a-brl
IPR002509, NODB_dom
IPR037950, PgdA-like
PfamiView protein in Pfam
PF01522, Polysacc_deac_1, 1 hit
SUPFAMiSSF88713, SSF88713, 1 hit
PROSITEiView protein in PROSITE
PS51677, NODB, 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 nameiPGDAE_HELPY
<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: O25080
<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: November 13, 2013
Last sequence update: January 1, 1998
Last modified: September 29, 2021
This is version 97 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

Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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