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Protein

N-acetylglucosamine-6-phosphate deacetylase

Gene

nagA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Enzyme 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

Manual assertion based on experiment ini

  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

    • N-acetylglucosamine-6-phosphate deacetylase activity Source: UniProtKB
    • zinc ion binding Source: UniProtKB

    GO - Biological processi

    • carbohydrate metabolic process Source: UniProtKB-KW
    • N-acetylglucosamine catabolic process Source: UniProtKB
    • N-acetylneuraminate catabolic process Source: EcoCyc
    • protein homotetramerization Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:NAG6PDEACET-MONOMER.
    ECOL316407:JW0663-MONOMER.
    MetaCyc:NAG6PDEACET-MONOMER.
    BRENDAi3.5.1.25. 2026.
    SABIO-RKP0AF18.
    UniPathwayiUPA00629; 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. 12 interactors.
    DIPiDIP-10297N.
    IntActiP0AF18. 5 interactors.
    STRINGi511145.b0677.

    Structurei

    Secondary structure

    1382
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 10Combined sources9
    Beta strandi15 – 24Combined sources10
    Beta strandi27 – 33Combined sources7
    Helixi34 – 36Combined sources3
    Beta strandi43 – 45Combined sources3
    Beta strandi50 – 53Combined sources4
    Beta strandi55 – 63Combined sources9
    Beta strandi66 – 71Combined sources6
    Turni72 – 74Combined sources3
    Helixi77 – 89Combined sources13
    Beta strandi92 – 100Combined sources9
    Helixi104 – 120Combined sources17
    Beta strandi123 – 125Combined sources3
    Beta strandi128 – 131Combined sources4
    Helixi137 – 139Combined sources3
    Helixi145 – 147Combined sources3
    Helixi150 – 161Combined sources12
    Turni162 – 165Combined sources4
    Beta strandi166 – 171Combined sources6
    Helixi173 – 175Combined sources3
    Helixi178 – 186Combined sources9
    Beta strandi190 – 193Combined sources4
    Helixi200 – 209Combined sources10
    Beta strandi213 – 216Combined sources4
    Turni217 – 220Combined sources4
    Helixi230 – 237Combined sources8
    Beta strandi242 – 246Combined sources5
    Beta strandi248 – 252Combined sources5
    Helixi254 – 264Combined sources11
    Helixi265 – 267Combined sources3
    Beta strandi268 – 271Combined sources4
    Turni276 – 279Combined sources4
    Beta strandi283 – 287Combined sources5
    Beta strandi290 – 294Combined sources5
    Beta strandi298 – 301Combined sources4
    Beta strandi306 – 309Combined sources4
    Helixi313 – 324Combined sources12
    Helixi328 – 335Combined sources8
    Helixi337 – 342Combined sources6
    Turni346 – 348Combined sources3
    Beta strandi349 – 351Combined sources3
    Beta strandi360 – 363Combined sources4
    Beta strandi369 – 374Combined sources6
    Beta strandi377 – 381Combined sources5

    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...

    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

    Belongs to the NagA family.Curated

    Phylogenomic databases

    eggNOGiENOG4105CE4. Bacteria.
    COG1820. LUCA.
    HOGENOMiHOG000275008.
    InParanoidiP0AF18.
    KOiK01443.
    OMAiPAGANMD.
    PhylomeDBiP0AF18.

    Family and domain databases

    CDDicd00854. NagA. 1 hit.
    Gene3Di2.30.40.10. 2 hits.
    InterProiIPR006680. Amidohydro-rel.
    IPR003764. GlcNAc_6-P_deAcase.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR032466. Metal_Hydrolase.
    [Graphical view]
    PfamiPF01979. Amidohydro_1. 1 hit.
    [Graphical view]
    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.
    PATRICi32116539. VBIEscCol129921_0702.

    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. 12 interactors.
    DIPiDIP-10297N.
    IntActiP0AF18. 5 interactors.
    STRINGi511145.b0677.

    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.
    PATRICi32116539. VBIEscCol129921_0702.

    Organism-specific databases

    EchoBASEiEB0626.
    EcoGeneiEG10632. nagA.

    Phylogenomic databases

    eggNOGiENOG4105CE4. Bacteria.
    COG1820. LUCA.
    HOGENOMiHOG000275008.
    InParanoidiP0AF18.
    KOiK01443.
    OMAiPAGANMD.
    PhylomeDBiP0AF18.

    Enzyme and pathway databases

    UniPathwayiUPA00629; UER00683.
    BioCyciEcoCyc:NAG6PDEACET-MONOMER.
    ECOL316407:JW0663-MONOMER.
    MetaCyc:NAG6PDEACET-MONOMER.
    BRENDAi3.5.1.25. 2026.
    SABIO-RKP0AF18.

    Miscellaneous databases

    EvolutionaryTraceiP0AF18.
    PROiP0AF18.

    Family and domain databases

    CDDicd00854. NagA. 1 hit.
    Gene3Di2.30.40.10. 2 hits.
    InterProiIPR006680. Amidohydro-rel.
    IPR003764. GlcNAc_6-P_deAcase.
    IPR011059. Metal-dep_hydrolase_composite.
    IPR032466. Metal_Hydrolase.
    [Graphical view]
    PfamiPF01979. Amidohydro_1. 1 hit.
    [Graphical view]
    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 historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: November 2, 2016
    This is version 90 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. 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.