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Protein

N-acetylglucosamine-6-phosphate deacetylase

Gene

nagA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Involved in the first step in the biosynthesis of amino-sugar-nucleotides. Catalyzes the hydrolysis of the N-acetyl group of N-acetylglucosamine-6-phosphate (GlcNAc-6-P) to yield glucosamine 6-phosphate and acetate. In vitro, can also hydrolyze substrate analogs such as N-thioacetyl-D-glucosamine-6-phosphate, N-trifluoroacetyl-D-glucosamine-6-phosphate, N-acetyl-D-glucosamine-6-sulfate, N-acetyl-D-galactosamine-6-phosphate, and N-formyl-D-glucosamine-6-phosphate.6 Publications

Catalytic activityi

N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate.5 Publications

Cofactori

Zn2+3 Publications, Co2+3 Publications, Mn2+3 Publications, Cd2+3 Publications, Fe2+3 Publications, Ni2+3 PublicationsNote: Binds 1 divalent metal cation per subunit. The highest efficient metals are Zn2+ and Co2+, followed by Mn2+, Cd2+, Fe2+ and Ni2+.3 Publications

Activity regulationi

Inhibited by high substrate concentration and by products glucosamine 6-phosphate and acetate. Completely inactivated by the treatment with 5,5'-dithio-bis(2-nitrobenzoate) or 2,2'-dithio-pyridine (2-DPDS). Inhibited by 1,10-phenanthroline and EDTA.4 Publications

Kineticsi

kcat is 102 sec(-1) for the deacetylation of N-acetyl-D-glucosamine-6-phosphate by the Zn-enzyme. The Cd-NagA catalyzes the hydrolysis of N-thioacetyl-D-glucosamine-6-phosphate substrate about an order of magnitude better than does the Zn-substituted enzyme. The N-trifluoroacetyl substituted substrate is hydrolyzed 26 times faster than the natural substrate, but the N-formyl substrate is hydrolyzed more slowly by a factor of 5.3 Publications
  1. KM=0.3 mM for N-acetyl-glucosamine 6-phosphate (at 30 degrees Celsius and pH 7.5)3 Publications
  2. KM=0.8 mM for N-acetyl-glucosamine 6-phosphate (at 37 degrees Celsius and pH 8.0)3 Publications
  3. KM=20 mM for glucosamine 6-phosphate (at 30 degrees Celsius and pH 7.5)3 Publications
  4. KM=20 mM for acetate (at 30 degrees Celsius and pH 7.5)3 Publications
  5. KM=0.08 mM for N-acetyl-D-glucosamine-6-phosphate (at 30 degrees Celsius and pH 7.5 using Zn-reconstituted form of the enzyme)3 Publications
  6. KM=1.24 mM for N-acetyl-D-galactosamine-6-phosphate (at 30 degrees Celsius and pH 7.5 using Zn-reconstituted form of the enzyme)3 Publications

    pH dependencei

    Optimum pH is 8.5.3 Publications

    Pathwayi: N-acetylneuraminate degradation

    This protein is involved in step 4 of the subpathway that synthesizes D-fructose 6-phosphate from N-acetylneuraminate.1 Publication
    Proteins known to be involved in the 5 steps of the subpathway in this organism are:
    1. N-acetylneuraminate lyase (nanA)
    2. N-acetylmannosamine kinase (nanK)
    3. Putative N-acetylmannosamine-6-phosphate 2-epimerase (nanE)
    4. N-acetylglucosamine-6-phosphate deacetylase (nagA)
    5. Glucosamine-6-phosphate deaminase (nagB)
    This subpathway is part of the pathway N-acetylneuraminate degradation, which is itself part of Amino-sugar metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-fructose 6-phosphate from N-acetylneuraminate, the pathway N-acetylneuraminate degradation and in Amino-sugar metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi131Zinc1 Publication1
    Metal bindingi195Zinc; via tele nitrogen1 Publication1
    Metal bindingi216Zinc; via tele nitrogen1 Publication1
    Binding sitei227Substrate1 Publication1
    Active sitei273Proton donor/acceptor1 Publication1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionHydrolase
    Biological processCarbohydrate metabolism
    LigandMetal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:NAG6PDEACET-MONOMER
    MetaCyc:NAG6PDEACET-MONOMER
    BRENDAi3.5.1.25 2026
    SABIO-RKiP0AF18
    UniPathwayi
    UPA00629;UER00683

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    N-acetylglucosamine-6-phosphate deacetylase1 Publication (EC:3.5.1.255 Publications)
    Short name:
    GlcNAc 6-P deacetylase1 Publication
    Gene namesi
    Name:nagA
    Ordered Locus Names:b0677, JW0663
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10632 nagA

    Pathology & Biotechi

    Disruption phenotypei

    Synthesizes high levels of glucosamine-6-phosphate deaminase and over half of the amount of glucosamine-6-phosphate synthase compared to wild-type.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi59Q → H: Large decrease in catalytic activity and substrate affinity, and increase in the average amount of Zn bound to the protein, suggesting that an additional metal ion can bind to this mutant; when associated with H-61. 2 Publications1
    Mutagenesisi61N → H: Large decrease in catalytic activity and substrate affinity, and increase in the average amount of Zn bound to the protein, suggesting that an additional metal ion can bind to this mutant; when associated with H-59. 1 Publication1
    Mutagenesisi131E → Q or A: Large reduction in the amount of the metal cofactor bound to the enzyme. 1 Publication1
    Mutagenesisi143H → N: Dramatic decrease in catalytic activity and moderate decrease in substrate affinity, producing a 6000-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi143H → Q: 180-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi251H → N: 500-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi273D → N or A: Loss of catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001709151 – 382N-acetylglucosamine-6-phosphate deacetylaseAdd BLAST382

    Proteomic databases

    EPDiP0AF18
    PaxDbiP0AF18
    PRIDEiP0AF18

    Expressioni

    Inductioni

    By N-acetylglucosamine. Induced by low extracellular levels of magnesium via the PhoQ/PhoP two-component regulatory system.1 Publication

    Interactioni

    Subunit structurei

    Homotetramer.4 Publications

    Protein-protein interaction databases

    BioGridi4261208, 26 interactors
    DIPiDIP-10297N
    IntActiP0AF18, 5 interactors
    STRINGi316385.ECDH10B_0742

    Structurei

    Secondary structure

    1382
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP0AF18
    SMRiP0AF18
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AF18

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni142 – 143Substrate binding1 Publication2
    Regioni219 – 220Substrate binding1 Publication2
    Regioni248 – 251Substrate binding1 Publication4
    Regioni306 – 308Substrate binding1 Publication3

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105CE4 Bacteria
    COG1820 LUCA
    HOGENOMiHOG000275008
    InParanoidiP0AF18
    KOiK01443
    OMAiHAFNAMP
    PhylomeDBiP0AF18

    Family and domain databases

    CDDicd00854 NagA, 1 hit
    Gene3Di2.30.40.10, 2 hits
    InterProiView protein in InterPro
    IPR006680 Amidohydro-rel
    IPR003764 GlcNAc_6-P_deAcase
    IPR011059 Metal-dep_hydrolase_composite
    IPR032466 Metal_Hydrolase
    PANTHERiPTHR11113:SF1 PTHR11113:SF1, 1 hit
    PfamiView protein in Pfam
    PF01979 Amidohydro_1, 1 hit
    PIRSFiPIRSF038994 NagA, 1 hit
    SUPFAMiSSF51338 SSF51338, 1 hit
    SSF51556 SSF51556, 1 hit
    TIGRFAMsiTIGR00221 nagA, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P0AF18-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MYALTQGRIF TGHEFLDDHA VVIADGLIKS VCPVAELPPE IEQRSLNGAI
    60 70 80 90 100
    LSPGFIDVQL NGCGGVQFND TAEAVSVETL EIMQKANEKS GCTNYLPTLI
    110 120 130 140 150
    TTSDELMKQG VRVMREYLAK HPNQALGLHL EGPWLNLVKK GTHNPNFVRK
    160 170 180 190 200
    PDAALVDFLC ENADVITKVT LAPEMVPAEV ISKLANAGIV VSAGHSNATL
    210 220 230 240 250
    KEAKAGFRAG ITFATHLYNA MPYITGREPG LAGAILDEAD IYCGIIADGL
    260 270 280 290 300
    HVDYANIRNA KRLKGDKLCL VTDATAPAGA NIEQFIFAGK TIYYRNGLCV
    310 320 330 340 350
    DENGTLSGSS LTMIEGVRNL VEHCGIALDE VLRMATLYPA RAIGVEKRLG
    360 370 380
    TLAAGKVANL TAFTPDFKIT KTIVNGNEVV TQ
    Length:382
    Mass (Da):40,949
    Last modified:December 20, 2005 - v1
    Checksum:iA10B015ADFC98FCA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X14135 Genomic DNA Translation: CAA32353.1
    AF052007 Genomic DNA Translation: AAC09325.1
    U00096 Genomic DNA Translation: AAC73771.1
    AP009048 Genomic DNA Translation: BAA35320.1
    PIRiA37018
    RefSeqiNP_415203.1, NC_000913.3
    WP_000271153.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC73771; AAC73771; b0677
    BAA35320; BAA35320; BAA35320
    GeneIDi945289
    KEGGiecj:JW0663
    eco:b0677
    PATRICifig|1411691.4.peg.1601

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X14135 Genomic DNA Translation: CAA32353.1
    AF052007 Genomic DNA Translation: AAC09325.1
    U00096 Genomic DNA Translation: AAC73771.1
    AP009048 Genomic DNA Translation: BAA35320.1
    PIRiA37018
    RefSeqiNP_415203.1, NC_000913.3
    WP_000271153.1, NZ_LN832404.1

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1YMYX-ray2.60A/B1-382[»]
    1YRRX-ray2.00A/B1-382[»]
    2P50X-ray2.20A/B/C/D1-382[»]
    2P53X-ray2.10A/B1-382[»]
    ProteinModelPortaliP0AF18
    SMRiP0AF18
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4261208, 26 interactors
    DIPiDIP-10297N
    IntActiP0AF18, 5 interactors
    STRINGi316385.ECDH10B_0742

    Proteomic databases

    EPDiP0AF18
    PaxDbiP0AF18
    PRIDEiP0AF18

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73771; AAC73771; b0677
    BAA35320; BAA35320; BAA35320
    GeneIDi945289
    KEGGiecj:JW0663
    eco:b0677
    PATRICifig|1411691.4.peg.1601

    Organism-specific databases

    EchoBASEiEB0626
    EcoGeneiEG10632 nagA

    Phylogenomic databases

    eggNOGiENOG4105CE4 Bacteria
    COG1820 LUCA
    HOGENOMiHOG000275008
    InParanoidiP0AF18
    KOiK01443
    OMAiHAFNAMP
    PhylomeDBiP0AF18

    Enzyme and pathway databases

    UniPathwayi
    UPA00629;UER00683

    BioCyciEcoCyc:NAG6PDEACET-MONOMER
    MetaCyc:NAG6PDEACET-MONOMER
    BRENDAi3.5.1.25 2026
    SABIO-RKiP0AF18

    Miscellaneous databases

    EvolutionaryTraceiP0AF18
    PROiPR:P0AF18

    Family and domain databases

    CDDicd00854 NagA, 1 hit
    Gene3Di2.30.40.10, 2 hits
    InterProiView protein in InterPro
    IPR006680 Amidohydro-rel
    IPR003764 GlcNAc_6-P_deAcase
    IPR011059 Metal-dep_hydrolase_composite
    IPR032466 Metal_Hydrolase
    PANTHERiPTHR11113:SF1 PTHR11113:SF1, 1 hit
    PfamiView protein in Pfam
    PF01979 Amidohydro_1, 1 hit
    PIRSFiPIRSF038994 NagA, 1 hit
    SUPFAMiSSF51338 SSF51338, 1 hit
    SSF51556 SSF51556, 1 hit
    TIGRFAMsiTIGR00221 nagA, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNAGA_ECOLI
    AccessioniPrimary (citable) accession number: P0AF18
    Secondary accession number(s): P15300
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: October 10, 2018
    This is version 101 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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