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Protein

N-acetylglucosamine-6-phosphate deacetylase

Gene

nagA

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the first committed 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.By similarity

Catalytic activityi

N-acetyl-D-glucosamine 6-phosphate + H2O = D-glucosamine 6-phosphate + acetate.By similarity

Cofactori

a divalent metal cation1 PublicationNote: Binds 1 divalent metal cation per subunit. Ni2+ ion is seen in the structure.1 Publication

Pathwayi: N-acetylneuraminate degradation

This protein is involved in step 4 of the subpathway that synthesizes D-fructose 6-phosphate from N-acetylneuraminate.Curated
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  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 bindingi128Divalent metal cation1 Publication1
Metal bindingi192Divalent metal cation; via tele nitrogen1 Publication1
Metal bindingi213Divalent metal cation; via tele nitrogen1 Publication1
Binding sitei224Substrate1 Publication1
Active sitei270Proton donor/acceptorBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Metal-binding, Nickel

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-16875.
VCHO:VC0994-MONOMER.
UniPathwayiUPA00629; UER00683.

Names & Taxonomyi

Protein namesi
Recommended name:
N-acetylglucosamine-6-phosphate deacetylaseBy similarity (EC:3.5.1.25By similarity)
Short name:
GlcNAc 6-P deacetylaseBy similarity
Gene namesi
Name:nagA
Ordered Locus Names:VC_0994
OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Taxonomic identifieri243277 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
Proteomesi
  • UP000000584 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001709181 – 378N-acetylglucosamine-6-phosphate deacetylaseAdd BLAST378

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi243277.VC0994.

Structurei

Secondary structure

1378
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 strandi42 – 53Combined sources12
Beta strandi55 – 60Combined sources6
Turni68 – 70Combined sources3
Helixi74 – 86Combined sources13
Beta strandi89 – 98Combined sources10
Helixi101 – 117Combined sources17
Beta strandi119 – 122Combined sources4
Beta strandi125 – 128Combined sources4
Helixi134 – 136Combined sources3
Turni142 – 144Combined sources3
Helixi150 – 158Combined sources9
Turni159 – 161Combined sources3
Beta strandi162 – 168Combined sources7
Helixi170 – 172Combined sources3
Helixi175 – 183Combined sources9
Beta strandi187 – 190Combined sources4
Helixi197 – 205Combined sources9
Beta strandi210 – 213Combined sources4
Beta strandi216 – 218Combined sources3
Helixi227 – 234Combined sources8
Beta strandi239 – 243Combined sources5
Beta strandi245 – 249Combined sources5
Helixi251 – 261Combined sources11
Helixi262 – 264Combined sources3
Beta strandi265 – 268Combined sources4
Turni273 – 276Combined sources4
Beta strandi280 – 286Combined sources7
Beta strandi288 – 292Combined sources5
Beta strandi295 – 297Combined sources3
Turni299 – 301Combined sources3
Helixi310 – 319Combined sources10
Helixi325 – 332Combined sources8
Helixi334 – 340Combined sources7
Turni343 – 345Combined sources3
Beta strandi346 – 348Combined sources3
Beta strandi357 – 360Combined sources4
Beta strandi366 – 371Combined sources6
Beta strandi374 – 377Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EGJX-ray2.90A/B1-378[»]
3IV8X-ray2.53A/B/C/D1-378[»]
ProteinModelPortaliO32445.
SMRiO32445.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO32445.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni139 – 140Substrate binding1 Publication2
Regioni216 – 217Substrate binding1 Publication2
Regioni245 – 248Substrate binding1 Publication4
Regioni303 – 305Substrate binding1 Publication3

Sequence similaritiesi

Belongs to the NagA family.Curated

Phylogenomic databases

eggNOGiENOG4105CE4. Bacteria.
COG1820. LUCA.
KOiK01443.
OMAiPAGANMD.

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.

O32445-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYALTNCKIY TGNDVLVKHA VIINGDKIEA VCPIESLPSE MNVVDLNGAN
60 70 80 90 100
LSPGFIDLQL NGCGGVMFND EITAETIDTM HKANLKSGCT SFLPTLITSS
110 120 130 140 150
DENMRQAIAA AREYQAKYPN QSLGLHLEGP YLNVMKKGIH SVDFIRPSDD
160 170 180 190 200
TMIDTICANS DVIAKVTLAP ENNKPEHIEK LVKAGIVVSI GHTNATYSEA
210 220 230 240 250
RKSFESGITF ATHLFNAMTP MVGREPGVVG AIYDTPEVYA GIIADGFHVD
260 270 280 290 300
YANIRIAHKI KGEKLVLVTD ATAPAGAEMD YFIFVGKKVY YRDGKCVDEN
310 320 330 340 350
GTLGGSALTM IEAVQNTVEH VGIALDEALR MATLYPAKAI GVDEKLGRIK
360 370
KGMIANLTVF DRDFNVKATV VNGQYEQN
Length:378
Mass (Da):40,956
Last modified:December 1, 2000 - v2
Checksum:i34906344A3F92A0F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti79T → I in BAA22834 (PubMed:9301118).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87820 Genomic DNA. Translation: BAA22834.1.
AE003852 Genomic DNA. Translation: AAF94155.1.
PIRiE82254.
JC5649.
RefSeqiNP_230640.1. NC_002505.1.
WP_000271133.1. NC_002505.1.

Genome annotation databases

EnsemblBacteriaiAAF94155; AAF94155; VC_0994.
GeneIDi2614247.
KEGGivch:VC0994.
PATRICi20081086. VBIVibCho83274_0947.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D87820 Genomic DNA. Translation: BAA22834.1.
AE003852 Genomic DNA. Translation: AAF94155.1.
PIRiE82254.
JC5649.
RefSeqiNP_230640.1. NC_002505.1.
WP_000271133.1. NC_002505.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EGJX-ray2.90A/B1-378[»]
3IV8X-ray2.53A/B/C/D1-378[»]
ProteinModelPortaliO32445.
SMRiO32445.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243277.VC0994.

Protocols and materials databases

DNASUi2614247.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF94155; AAF94155; VC_0994.
GeneIDi2614247.
KEGGivch:VC0994.
PATRICi20081086. VBIVibCho83274_0947.

Phylogenomic databases

eggNOGiENOG4105CE4. Bacteria.
COG1820. LUCA.
KOiK01443.
OMAiPAGANMD.

Enzyme and pathway databases

UniPathwayiUPA00629; UER00683.
BioCyciMetaCyc:MONOMER-16875.
VCHO:VC0994-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO32445.

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_VIBCH
AccessioniPrimary (citable) accession number: O32445
Secondary accession number(s): Q9KTA9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: December 1, 2000
Last modified: November 2, 2016
This is version 103 of the entry and version 2 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. 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

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.