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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

Manual assertion based on experiment ini

  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

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Virulence

    Keywords - Ligandi

    Cobalt, Metal-binding, Zinc

    Enzyme and pathway databases

    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

    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)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
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi47 – 61Combined sources15
    Beta strandi65 – 72Combined sources8
    Beta strandi75 – 84Combined sources10
    Helixi90 – 102Combined sources13
    Beta strandi110 – 119Combined sources10
    Beta strandi125 – 135Combined sources11
    Beta strandi138 – 141Combined sources4
    Beta strandi144 – 156Combined sources13
    Helixi164 – 167Combined sources4
    Helixi171 – 184Combined sources14
    Helixi208 – 210Combined sources3
    Beta strandi213 – 216Combined sources4
    Beta strandi219 – 222Combined sources4
    Beta strandi234 – 237Combined sources4
    Helixi238 – 244Combined sources7
    Helixi247 – 249Combined sources3
    Helixi252 – 265Combined sources14
    Beta strandi269 – 276Combined sources8
    Turni280 – 282Combined sources3
    Helixi283 – 292Combined sources10
    Beta strandi298 – 301Combined sources4
    Helixi303 – 305Combined sources3
    Turni306 – 308Combined sources3
    Helixi310 – 318Combined sources9
    Beta strandi322 – 325Combined sources4
    Helixi333 – 335Combined sources3
    Helixi338 – 356Combined sources19
    Helixi366 – 368Combined sources3
    Helixi372 – 376Combined sources5
    Beta strandi381 – 383Combined sources3
    Beta strandi386 – 388Combined sources3
    Helixi391 – 394Combined sources4
    Helixi397 – 407Combined sources11
    Beta strandi412 – 417Combined sources6
    Helixi421 – 436Combined sources16
    Helixi444 – 448Combined sources5
    Helixi449 – 451Combined sources3
    Beta strandi457 – 461Combined sources5

    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...

    Miscellaneous databases

    EvolutionaryTraceiQ8DP63.

    Family & Domainsi

    Domains and Repeats

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

    Sequence similaritiesi

    Contains 1 NodB homology domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

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

    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
    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.
    PATRICi19702660. VBIStrPne107296_1445.

    Phylogenomic databases

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

    Enzyme and pathway databases

    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...

    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: November 2, 2016
    This is version 89 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.