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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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi128 – 1281Divalent metal cation1 Publication
Metal bindingi192 – 1921Divalent metal cation; via tele nitrogen1 Publication
Metal bindingi213 – 2131Divalent metal cation; via tele nitrogen1 Publication
Binding sitei224 – 2241Substrate1 Publication
Active sitei270 – 2701Proton donor/acceptorBy similarity

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.
RETL1328306-WGS:GSTH-4130-MONOMER.
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 378378N-acetylglucosamine-6-phosphate deacetylasePRO_0000170918Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi243277.VC0994.

Structurei

Secondary structure

1
378
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 109Combined sources
Beta strandi15 – 2410Combined sources
Beta strandi27 – 337Combined sources
Helixi34 – 363Combined sources
Beta strandi42 – 5312Combined sources
Beta strandi55 – 606Combined sources
Turni68 – 703Combined sources
Helixi74 – 8613Combined sources
Beta strandi89 – 9810Combined sources
Helixi101 – 11717Combined sources
Beta strandi119 – 1224Combined sources
Beta strandi125 – 1284Combined sources
Helixi134 – 1363Combined sources
Turni142 – 1443Combined sources
Helixi150 – 1589Combined sources
Turni159 – 1613Combined sources
Beta strandi162 – 1687Combined sources
Helixi170 – 1723Combined sources
Helixi175 – 1839Combined sources
Beta strandi187 – 1904Combined sources
Helixi197 – 2059Combined sources
Beta strandi210 – 2134Combined sources
Beta strandi216 – 2183Combined sources
Helixi227 – 2348Combined sources
Beta strandi239 – 2435Combined sources
Beta strandi245 – 2495Combined sources
Helixi251 – 26111Combined sources
Helixi262 – 2643Combined sources
Beta strandi265 – 2684Combined sources
Turni273 – 2764Combined sources
Beta strandi280 – 2867Combined sources
Beta strandi288 – 2925Combined sources
Beta strandi295 – 2973Combined sources
Turni299 – 3013Combined sources
Helixi310 – 31910Combined sources
Helixi325 – 3328Combined sources
Helixi334 – 3407Combined sources
Turni343 – 3453Combined sources
Beta strandi346 – 3483Combined sources
Beta strandi357 – 3604Combined sources
Beta strandi366 – 3716Combined sources
Beta strandi374 – 3774Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EGJX-ray2.90A/B1-378[»]
3IV8X-ray2.53A/B/C/D1-378[»]
ProteinModelPortaliO32445.
SMRiO32445. Positions 1-373.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO32445.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni139 – 1402Substrate binding1 Publication
Regioni216 – 2172Substrate binding1 Publication
Regioni245 – 2484Substrate binding1 Publication
Regioni303 – 3053Substrate binding1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti79 – 791T → I in BAA22834 (PubMed:9301118).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
3EGJX-ray2.90A/B1-378[»]
3IV8X-ray2.53A/B/C/D1-378[»]
ProteinModelPortaliO32445.
SMRiO32445. Positions 1-373.
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.
RETL1328306-WGS:GSTH-4130-MONOMER.
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: September 7, 2016
This is version 101 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.