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Protein

Peptidoglycan-N-acetylglucosamine deacetylase

Gene

pgdA

Organism
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the deacetylation of N-acetylglucosamine (GlcNAc) residues in peptidoglycan, a modification that confers host lysozyme resistance and contributes to pneumococcal virulence.3 Publications

Catalytic activityi

Peptidoglycan-N-acetyl-D-glucosamine + H2O = peptidoglycan-D-glucosamine + acetate.2 Publications

Cofactori

Zn2+1 Publication, Co2+1 PublicationNote: Zn2+. Although displays higher activity with Co2+ than with Zn2+ in vitro, bioavailability may well limit this enzyme to be zinc-dependent.1 Publication

Activity regulationi

Enzymatic activity is inhibited by EDTA in vitro.1 Publication

Kineticsi

kcat is 0.55 sec(-1) with GlcNAc3 as substrate.1 Publication
  1. KM=3.8 mM for GlcNAc31 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei275Proton acceptor1 Publication1
    Metal bindingi276Zinc1 Publication1
    Metal bindingi326Zinc; via tele nitrogen1 Publication1
    Metal bindingi330Zinc; via tele nitrogen1 Publication1
    Binding sitei367Substrate; via amide nitrogen1 Publication1
    Sitei391Raises pKa of active site His1 Publication1
    Active sitei417Proton donor1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase
    Biological processCarbohydrate metabolism, Virulence
    LigandCobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciSPNE171101:SPR1333-MONOMER
    BRENDAi3.5.1.104 1960

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptidoglycan-N-acetylglucosamine deacetylase1 Publication (EC:3.5.1.1042 Publications)
    Short name:
    Peptidoglycan GlcNAc deacetylaseCurated
    Alternative name(s):
    Peptidoglycan N-deacetylase1 Publication
    Short name:
    PG N-deacetylaseCurated
    Gene namesi
    Name:pgdA1 Publication
    Ordered Locus Names:spr1333
    OrganismiStreptococcus pneumoniae (strain ATCC BAA-255 / R6)
    Taxonomic identifieri171101 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
    Proteomesi
    • UP000000586 Componenti: Chromosome

    Subcellular locationi

    Topology

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transmembranei18 – 38HelicalSequence analysisAdd BLAST21

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene produce fully N-acetylated glycan, become hypersensitive to exogenous lysozyme in the stationary phase of growth, and show reduced virulence in the intraperitoneal mouse model.2 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi275D → N: Loss of activity. 1 Publication1
    Mutagenesisi326H → A: Loss of activity. 1 Publication1
    Mutagenesisi364R → S: Loss of activity. 1 Publication1
    Mutagenesisi391D → N: Loss of activity. 1 Publication1
    Mutagenesisi417H → S: Loss of activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004244401 – 463Peptidoglycan-N-acetylglucosamine deacetylaseAdd BLAST463

    Interactioni

    Protein-protein interaction databases

    STRINGi171101.spr1333

    Chemistry databases

    BindingDBiQ8DP63

    Structurei

    Secondary structure

    1463
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliQ8DP63
    SMRiQ8DP63
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8DP63

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini268 – 442NodB homologyPROSITE-ProRule annotationAdd BLAST175

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiENOG4108ZJ4 Bacteria
    COG0726 LUCA
    HOGENOMiHOG000235351
    KOiK22278
    OMAiFFMMGSK

    Family and domain databases

    InterProiView protein in InterPro
    IPR011330 Glyco_hydro/deAcase_b/a-brl
    IPR002509 NODB_dom
    IPR017219 Peptidoglycan_deacetylase
    PfamiView protein in Pfam
    PF01522 Polysacc_deac_1, 1 hit
    PIRSFiPIRSF037479 PG_GlcNAc_deacetylase, 1 hit
    SUPFAMiSSF88713 SSF88713, 1 hit
    PROSITEiView protein in PROSITE
    PS51677 NODB, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Q8DP63-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MNKSRLGRGR HGKTRHVLLA LIGILAISIC LLGGFIAFKI YQQKSFEQKI
    60 70 80 90 100
    ESLKKEKDDQ LSEGNQKEHF RQGQAEVIAY YPLQGEKVIS SVRELINQDV
    110 120 130 140 150
    KDKLESKDNL VFYYTEQEES GLKGVVNRNV TKQIYDLVAF KIEETEKTSL
    160 170 180 190 200
    GKVHLTEDGQ PFTLDQLFSD ASKAKEQLIK ELTSFIEDKK IEQDQSEQIV
    210 220 230 240 250
    KNFSDQDLSA WNFDYKDSQI ILYPSPVVEN LEEIALPVSA FFDVIQSSYL
    260 270 280 290 300
    LEKDAALYQS YFDKKHQKVV ALTFDDGPNP ATTPQVLETL AKYDIKATFF
    310 320 330 340 350
    VLGKNVSGNE DLVKRIKSEG HVVGNHSWSH PILSQLSLDE AKKQITDTED
    360 370 380 390 400
    VLTKVLGSSS KLMRPPYGAI TDDIRNSLDL SFIMWDVDSL DWKSKNEASI
    410 420 430 440 450
    LTEIQHQVAN GSIVLMHDIH SPTVNALPRV IEYLKNQGYT FVTIPEMLNT
    460
    RLKAHELYYS RDE
    Length:463
    Mass (Da):52,675
    Last modified:March 1, 2003 - v1
    Checksum:i12E1935E66521EDE
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE007317 Genomic DNA Translation: AAL00137.1
    PIRiD98038
    RefSeqiNP_358926.1, NC_003098.1
    WP_001854799.1, NC_003098.1

    Genome annotation databases

    EnsemblBacteriaiAAL00137; AAL00137; spr1333
    GeneIDi934547
    KEGGispr:spr1333
    PATRICifig|171101.6.peg.1445

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE007317 Genomic DNA Translation: AAL00137.1
    PIRiD98038
    RefSeqiNP_358926.1, NC_003098.1
    WP_001854799.1, NC_003098.1

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2C1GX-ray1.75A38-463[»]
    2C1IX-ray1.35A38-463[»]
    ProteinModelPortaliQ8DP63
    SMRiQ8DP63
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi171101.spr1333

    Chemistry databases

    BindingDBiQ8DP63

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL00137; AAL00137; spr1333
    GeneIDi934547
    KEGGispr:spr1333
    PATRICifig|171101.6.peg.1445

    Phylogenomic databases

    eggNOGiENOG4108ZJ4 Bacteria
    COG0726 LUCA
    HOGENOMiHOG000235351
    KOiK22278
    OMAiFFMMGSK

    Enzyme and pathway databases

    BioCyciSPNE171101:SPR1333-MONOMER
    BRENDAi3.5.1.104 1960

    Miscellaneous databases

    EvolutionaryTraceiQ8DP63

    Family and domain databases

    InterProiView protein in InterPro
    IPR011330 Glyco_hydro/deAcase_b/a-brl
    IPR002509 NODB_dom
    IPR017219 Peptidoglycan_deacetylase
    PfamiView protein in Pfam
    PF01522 Polysacc_deac_1, 1 hit
    PIRSFiPIRSF037479 PG_GlcNAc_deacetylase, 1 hit
    SUPFAMiSSF88713 SSF88713, 1 hit
    PROSITEiView protein in PROSITE
    PS51677 NODB, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPGDA_STRR6
    AccessioniPrimary (citable) accession number: Q8DP63
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 13, 2013
    Last sequence update: March 1, 2003
    Last modified: September 12, 2018
    This is version 96 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    UniProt is an ELIXIR core data resource
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