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Protein

Peptidoglycan-N-acetylglucosamine deacetylase

Gene

pgdA

Organism
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Enzyme 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)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei275 – 2751Proton acceptor1 Publication
    Metal bindingi276 – 2761Zinc1 Publication
    Metal bindingi326 – 3261Zinc; via tele nitrogen1 Publication
    Metal bindingi330 – 3301Zinc; via tele nitrogen1 Publication
    Binding sitei367 – 3671Substrate; via amide nitrogen1 Publication
    Sitei391 – 3911Raises pKa of active site His1 Publication
    Active sitei417 – 4171Proton donor1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Virulence

    Keywords - Ligandi

    Cobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciSPNE171101:GJC8-1346-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)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei18 – 3821HelicalSequence analysisAdd
    BLAST

    GO - Cellular componenti

    Complete GO annotation...

    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi275 – 2751D → N: Loss of activity. 1 Publication
    Mutagenesisi326 – 3261H → A: Loss of activity. 1 Publication
    Mutagenesisi364 – 3641R → S: Loss of activity. 1 Publication
    Mutagenesisi391 – 3911D → N: Loss of activity. 1 Publication
    Mutagenesisi417 – 4171H → S: Loss of activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 463463Peptidoglycan-N-acetylglucosamine deacetylasePRO_0000424440Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi171101.spr1333.

    Structurei

    Secondary structure

    1
    463
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi47 – 6115Combined sources
    Beta strandi65 – 728Combined sources
    Beta strandi75 – 8410Combined sources
    Helixi90 – 10213Combined sources
    Beta strandi110 – 11910Combined sources
    Beta strandi125 – 13511Combined sources
    Beta strandi138 – 1414Combined sources
    Beta strandi144 – 15613Combined sources
    Helixi164 – 1674Combined sources
    Helixi171 – 18414Combined sources
    Helixi208 – 2103Combined sources
    Beta strandi213 – 2164Combined sources
    Beta strandi219 – 2224Combined sources
    Beta strandi234 – 2374Combined sources
    Helixi238 – 2447Combined sources
    Helixi247 – 2493Combined sources
    Helixi252 – 26514Combined sources
    Beta strandi269 – 2768Combined sources
    Turni280 – 2823Combined sources
    Helixi283 – 29210Combined sources
    Beta strandi298 – 3014Combined sources
    Helixi303 – 3053Combined sources
    Turni306 – 3083Combined sources
    Helixi310 – 3189Combined sources
    Beta strandi322 – 3254Combined sources
    Helixi333 – 3353Combined sources
    Helixi338 – 35619Combined sources
    Helixi366 – 3683Combined sources
    Helixi372 – 3765Combined sources
    Beta strandi381 – 3833Combined sources
    Beta strandi386 – 3883Combined sources
    Helixi391 – 3944Combined sources
    Helixi397 – 40711Combined sources
    Beta strandi412 – 4176Combined sources
    Helixi421 – 43616Combined sources
    Helixi444 – 4485Combined sources
    Helixi449 – 4513Combined sources
    Beta strandi457 – 4615Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C1GX-ray1.75A38-463[»]
    2C1IX-ray1.35A38-463[»]
    ProteinModelPortaliQ8DP63.
    SMRiQ8DP63. Positions 46-463.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8DP63.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini268 – 442175NodB homologyPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 NodB homology domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiENOG4108ZJ4. Bacteria.
    COG0726. LUCA.
    HOGENOMiHOG000235351.
    OMAiFFMMGSK.
    OrthoDBiEOG6V1M8Q.

    Family and domain databases

    Gene3Di3.20.20.370. 1 hit.
    InterProiIPR011330. Glyco_hydro/deAcase_b/a-brl.
    IPR002509. NODB_dom.
    IPR017219. Peptidoglycan_deacetylase.
    [Graphical view]
    PfamiPF01522. Polysacc_deac_1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037479. PG_GlcNAc_deacetylase. 1 hit.
    SUPFAMiSSF88713. SSF88713. 1 hit.
    PROSITEiPS51677. NODB. 1 hit.
    [Graphical view]

    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.
    PATRICi19702660. VBIStrPne107296_1445.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2C1GX-ray1.75A38-463[»]
    2C1IX-ray1.35A38-463[»]
    ProteinModelPortaliQ8DP63.
    SMRiQ8DP63. Positions 46-463.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi171101.spr1333.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAL00137; AAL00137; spr1333.
    GeneIDi934547.
    KEGGispr:spr1333.
    PATRICi19702660. VBIStrPne107296_1445.

    Phylogenomic databases

    eggNOGiENOG4108ZJ4. Bacteria.
    COG0726. LUCA.
    HOGENOMiHOG000235351.
    OMAiFFMMGSK.
    OrthoDBiEOG6V1M8Q.

    Enzyme and pathway databases

    BioCyciSPNE171101:GJC8-1346-MONOMER.
    BRENDAi3.5.1.104. 1960.

    Miscellaneous databases

    EvolutionaryTraceiQ8DP63.

    Family and domain databases

    Gene3Di3.20.20.370. 1 hit.
    InterProiIPR011330. Glyco_hydro/deAcase_b/a-brl.
    IPR002509. NODB_dom.
    IPR017219. Peptidoglycan_deacetylase.
    [Graphical view]
    PfamiPF01522. Polysacc_deac_1. 1 hit.
    [Graphical view]
    PIRSFiPIRSF037479. PG_GlcNAc_deacetylase. 1 hit.
    SUPFAMiSSF88713. SSF88713. 1 hit.
    PROSITEiPS51677. NODB. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC BAA-255 / R6.
    2. "The pgdA gene encodes for a peptidoglycan N-acetylglucosamine deacetylase in Streptococcus pneumoniae."
      Vollmer W., Tomasz A.
      J. Biol. Chem. 275:20496-20501(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, GENE NAME, DISRUPTION PHENOTYPE.
      Strain: R36A.
    3. "Peptidoglycan N-acetylglucosamine deacetylase, a putative virulence factor in Streptococcus pneumoniae."
      Vollmer W., Tomasz A.
      Infect. Immun. 70:7176-7178(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: R36A.
    4. "Structure and metal-dependent mechanism of peptidoglycan deacetylase, a streptococcal virulence factor."
      Blair D.E., Schuttelkopf A.W., MacRae J.I., van Aalten D.M.
      Proc. Natl. Acad. Sci. U.S.A. 102:15429-15434(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) OF 38-463 OF WILD-TYPE AND MUTANT ASN-275 IN COMPLEX WITH ACETATE PRODUCT AND ZINC, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, ACTIVE SITE, MUTAGENESIS OF ASP-275; HIS-326; ARG-364; ASP-391 AND HIS-417.

    Entry informationi

    Entry nameiPGDA_STRR6
    AccessioniPrimary (citable) accession number: Q8DP63
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 13, 2013
    Last sequence update: March 1, 2003
    Last modified: December 9, 2015
    This is version 85 of the entry and version 1 of the sequence. [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
    2. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.