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Entry version 115 (02 Dec 2020)
Sequence version 1 (01 Jan 1998)
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Protein

Peptidoglycan-N-acetylmuramic acid deacetylase PdaC

Gene

pdaC

Organism
Bacillus subtilis (strain 168)
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 deacetylation of N-acetylmuramic acid (MurNAc) residues in peptidoglycan, a modification that confers resistance to lysosyme. Is not able to deacetylate N-acetylglucosamine (GlcNAc) residues in peptidoglycan, but can deacylate chitin oligomers such as GlcNAc4 and GlcNAc5. Is essentially not active toward chitosan (partially deacetylated GlcNAc polymer) and has very low activity toward chitin (GlcNAc polymer). Does not deacetylate GlcNAc.1 Publication

Miscellaneous

The product of deacetylated GlcNAc4 by PdaC is GlcNAc-GlcNAc-GlcN-GlcNAc.1 Publication
Derepression of pdaC in cells depleted for yycFG leads to increased resistance of the cell walls to lysozyme digestion.

Caution

Was originally described as a deoxyribonuclease (PubMed:17878218), but it was later shown that PdaC has no DNase activity at all (PubMed:22277649).2 Publications

<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

Activated by divalent metal cations; Mn2+ is the most efficient, followed by Ca2+ and Mg2+. In contrast to PgdA from S.pneumoniae, these ions are not absolutely required for deacetylase activity.1 Publication

<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 0.32 sec(-1) for the deacetylation of MurNAc residues in peptidoglycan, and 0.24 sec(-1) for the deacetylation of GlcNAc4.
  1. KM=4.8 mM for non-treated B.subtilis peptidoglycan1 Publication
  2. KM=12.3 mM for GlcNAc41 Publication

    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 sitei285Proton acceptorBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 bindingi286Divalent metal cationBy similarity1
    Metal bindingi336Divalent metal cation; via tele nitrogenBy similarity1
    Metal bindingi340Divalent metal cation; via tele nitrogenBy similarity1
    <p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei401Raises pKa of active site HisBy similarity1
    Active sitei427Proton donorBy 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
    LigandMetal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    BSUB:BSU12100-MONOMER

    <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:
    Peptidoglycan-N-acetylmuramic acid deacetylase PdaC (EC:3.5.1.-)
    Short name:
    Peptidoglycan MurNAc deacetylase
    Alternative name(s):
    Polysaccharide deacetylase PdaC
    <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:pdaC
    Synonyms:yjeA
    Ordered Locus Names:BSU12100
    <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>OrganismiBacillus subtilis (strain 168)
    <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 identifieri224308 [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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    <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
    • UP000001570 <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

    Topology

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei6 – 26HelicalSequence analysisAdd BLAST21

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cell membrane, Membrane

    <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 show sensitivity to lysosyme, in contrast to wild-type.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_00000248461 – 467Peptidoglycan-N-acetylmuramic acid deacetylase PdaCAdd BLAST467

    Proteomic databases

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

    More...
    PaxDbi
    O34798

    PRoteomics IDEntifications database

    More...
    PRIDEi
    O34798

    <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

    Negatively regulated by the two-component system YycFG.1 Publication

    <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

    Protein interaction database and analysis system

    More...
    IntActi
    O34798, 2 interactors

    STRING: functional protein association networks

    More...
    STRINGi
    224308.BSU12100

    <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

    1467
    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
    O34798

    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

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">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>Domaini278 – 452NodB homologyPROSITE-ProRule annotationAdd BLAST175

    <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

    In the N-terminal section; belongs to the RsiV family.Curated
    In the C-terminal section; belongs to the polysaccharide deacetylase family.Curated

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG0726, Bacteria

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    VQYYPET

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.90.640.20, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR021729, DUF3298
    IPR011330, Glyco_hydro/deAcase_b/a-brl
    IPR002509, NODB_dom
    IPR025303, PdaC
    IPR037126, PdaC/RsiV-like_sf
    IPR017219, Peptidoglycan_deacetylase

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF11738, DUF3298, 1 hit
    PF13739, PdaC, 1 hit
    PF01522, Polysacc_deac_1, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF037479, PG_GlcNAc_deacetylase, 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%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.

    O34798-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MLAKRIKWFH VLIAVVCVVG LIGFFHNHSL KKETVMNKVR TDSQYGNVEI
    60 70 80 90 100
    ATLVNDGKTF NYAVNYPVFK NEKMDSALKR FAEKEVRQFQ KETKDVDQEH
    110 120 130 140 150
    TTKRNELNVD YKIVHYAKQT VAIVFNEYKY IGGAHGQTVK KTFNYDFSKQ
    160 170 180 190 200
    AFLSIDDIFK EDADYLHKLS LIAYHELKKN KDIAADDALL KEGTAPKKEN
    210 220 230 240 250
    FSRFAIKEDY IELYFDTYQV AAGYLGEQSI AIKKSLLKDI LKEQYIDKAK
    260 270 280 290 300
    NKNKIKEQKP KHEVISLPKE ETVDPNQKVI ALTFDDGPNP ATTNQILDSL
    310 320 330 340 350
    KKYKGHATFF VLGSRVQYYP ETLIRMLKEG NEVGNHSWSH PLLTRLSVKE
    360 370 380 390 400
    ALKQINDTQD IIEKISGYRP TLVRPPYGGI NDELRSQMKM DVALWDVDPE
    410 420 430 440 450
    DWKDRNKKTI VDRVMNQAGD GRTILIHDIY RTSADAADEI IKKLTDQGYQ
    460
    LVTVSQLEEV KKQREAK
    Length:467
    Mass (Da):53,839
    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:i95D2B1245968F804
    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
    AF015825 Genomic DNA Translation: AAC46306.1
    AL009126 Genomic DNA Translation: CAB13067.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    G69849

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_389092.1, NC_000964.3
    WP_003245023.1, NZ_JNCM01000035.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAB13067; CAB13067; BSU12100

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    936440

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    bsu:BSU12100

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|224308.179.peg.1307

    <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
    AF015825 Genomic DNA Translation: AAC46306.1
    AL009126 Genomic DNA Translation: CAB13067.1
    PIRiG69849
    RefSeqiNP_389092.1, NC_000964.3
    WP_003245023.1, NZ_JNCM01000035.1

    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
    6H8LX-ray1.54A/B270-467[»]
    6H8NX-ray1.26A/B270-467[»]
    SMRiO34798
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    IntActiO34798, 2 interactors
    STRINGi224308.BSU12100

    Proteomic databases

    PaxDbiO34798
    PRIDEiO34798

    Genome annotation databases

    EnsemblBacteriaiCAB13067; CAB13067; BSU12100
    GeneIDi936440
    KEGGibsu:BSU12100
    PATRICifig|224308.179.peg.1307

    Phylogenomic databases

    eggNOGiCOG0726, Bacteria
    OMAiVQYYPET

    Enzyme and pathway databases

    BioCyciBSUB:BSU12100-MONOMER

    Family and domain databases

    Gene3Di3.90.640.20, 1 hit
    InterProiView protein in InterPro
    IPR021729, DUF3298
    IPR011330, Glyco_hydro/deAcase_b/a-brl
    IPR002509, NODB_dom
    IPR025303, PdaC
    IPR037126, PdaC/RsiV-like_sf
    IPR017219, Peptidoglycan_deacetylase
    PfamiView protein in Pfam
    PF11738, DUF3298, 1 hit
    PF13739, PdaC, 1 hit
    PF01522, Polysacc_deac_1, 1 hit
    PIRSFiPIRSF037479, PG_GlcNAc_deacetylase, 1 hit
    SUPFAMiSSF88713, SSF88713, 1 hit
    PROSITEiView protein in PROSITE
    PS51677, NODB, 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 nameiPDAC_BACSU
    <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: O34798
    <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: November 25, 2002
    Last sequence update: January 1, 1998
    Last modified: December 2, 2020
    This is version 115 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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