EzCatDB: D00801
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DB codeD00801
RLCP classification1.13.7495.453 : Hydrolysis
CATH domainDomain 12.30.40.10 : Urease, subunit C; domain 1
Domain 23.20.20.140 : TIM BarrelCatalytic domain
E.C.3.5.1.25

CATH domainRelated DB codes (homologues)
2.30.40.10 : Urease, subunit C; domain 1D00673,D00675,D00873,M00030,M00225,M00226
3.20.20.140 : TIM BarrelS00231,S00232,M00186,D00673,D00675,D00873,M00030,M00225,M00226

Enzyme Name
UniProtKBKEGG

P0AF18
Protein nameN-acetylglucosamine-6-phosphate deacetylaseN-Acetylglucosamine-6-phosphate deacetylase
Acetylglucosamine phosphate deacetylase
Acetylaminodeoxyglucosephosphate acetylhydrolase
2-Acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase
SynonymsEC 3.5.1.25
GlcNAc 6-P deacetylase
RefSeqNP_415203.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488957.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01979 (Amidohydro_1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00530Aminosugars metabolism

UniProtKB:Accession NumberP0AF18
Entry nameNAGA_ECOLI
ActivityN-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00038C00357C00001C00352C00033I00110
CompoundZincN-acetyl-D-glucosamine 6-phosphateH2OD-glucosamine 6-phosphateacetateN-tetrahedral intermediate of N-acetyl-D-glucosamine 6-phosphate
Typeheavy metalamide group,carbohydrate,phosphate group/phosphate ionH2Oamine group,carbohydrate,phosphate group/phosphate ioncarboxyl group
ChEBI29105
15784
15377
47987
15366

PubChem32051
440996
962
22247451
440997
21980959
176

              
1ymyA01UnboundUnbound UnboundUnboundUnbound
1ymyB01UnboundUnbound UnboundUnboundUnbound
1yrrA01UnboundUnbound UnboundUnboundUnbound
1yrrB01UnboundUnbound UnboundUnboundUnbound
2p50A01UnboundUnbound UnboundUnboundUnbound
2p50B01UnboundUnbound UnboundUnboundUnbound
2p50C01UnboundUnbound UnboundUnboundUnbound
2p50D01UnboundUnbound UnboundUnboundUnbound
2p53A01UnboundUnbound UnboundUnboundUnbound
2p53B01UnboundUnbound UnboundUnboundUnbound
1ymyA02UnboundUnbound UnboundUnboundUnbound
1ymyB02UnboundUnbound UnboundUnboundUnbound
1yrrA02UnboundUnbound UnboundUnboundUnbound
1yrrB02UnboundUnbound UnboundUnboundUnbound
2p50A02Bound:_ZNUnbound UnboundUnboundUnbound
2p50B02Bound:_ZNUnbound UnboundUnboundUnbound
2p50C02Bound:_ZNUnbound UnboundUnboundUnbound
2p50D02Bound:_ZNUnbound UnboundUnboundUnbound
2p53A02Bound:_ZNUnbound UnboundUnboundTransition-state-analogue:NNG
2p53B02Bound:_ZNUnbound UnboundUnboundTransition-state-analogue:NNG

Active-site residues
resource
2p50, 2p53 & literature [4]
pdbCatalytic residuesCofactor-binding residuescomment
           
1ymyA01 
 
 
1ymyB01 
 
 
1yrrA01 
 
 
1yrrB01 
 
 
2p50A01 
 
 
2p50B01 
 
 
2p50C01 
 
 
2p50D01 
 
 
2p53A01 
 
 
2p53B01 
 
 
1ymyA02       ;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
invisible 139-144
1ymyB02       ;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
invisible 138-152
1yrrA02HIS 143;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
invisible 141
1yrrB02       ;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
invisible 137-152
2p50A02HIS 143;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
 
2p50B02HIS 143;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
 
2p50C02HIS 143;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
 
2p50D02HIS 143;ASP 273
GLU 131;HIS 195;HIS 216(Zinc binding)
 
2p53A02HIS 143;       
GLU 131;HIS 195;HIS 216(Zinc binding)
mutant D273N
2p53B02HIS 143;       
GLU 131;HIS 195;HIS 216(Zinc binding)
mutant D273N

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p. 317
[5]Fig.5, p.7951

references
[1]
PubMed ID9143339
JournalArch Biochem Biophys
Year1997
Volume340
Pages338-46
AuthorsSouza JM, Plumbridge JA, Calcagno ML
TitleN-acetylglucosamine-6-phosphate deacetylase from Escherichia coli: purification and molecular and kinetic characterization.
[2]
PubMed ID15850372
JournalBiochemistry
Year2005
Volume44
Pages6383-91
AuthorsSeibert CM, Raushel FM
TitleStructural and catalytic diversity within the amidohydrolase superfamily.
[3]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID16630633
JournalJ Mol Biol
Year2006
Volume359
Pages308-21
AuthorsFerreira FM, Mendoza-Hernandez G, Castaneda-Bueno M, Aparicio R, Fischer H, Calcagno ML, Oliva G
TitleStructural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli.
Related PDB1yrr
[4]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID17567048
JournalBiochemistry
Year2007
Volume46
Pages7953-62
AuthorsHall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM
TitleStructural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.
Related PDB2p50,2p53
[5]
PubMed ID17567047
JournalBiochemistry
Year2007
Volume46
Pages7942-52
AuthorsHall RS, Xiang DF, Xu C, Raushel FM
TitleN-Acetyl-D-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion.

comments
This enzyme belongs to amidohydrolase superfamily.
According to the literature [4] and [5], the reaction proceeds as follows:
(0) A hydrolytic water or hydroxide is bound to Asp273 and a zinc ion, which is bound to Glu131, His195 and His216. The carbonyl oxygen of the scissile bond or amide bond of the substrate is hydrogen bonded to His143 and the zinc ion. Thus, the water and scissile bond can be activated by the zinc ion.
(1) Asp273 acts as a general base to deprotonate the water, to activate it.
(2) The activated water makes a nucleophilic attack on the carbonyl carbon of the amide group, forming a tetrahedral intermediate. This intermediate can be stabilized by His143 and the zinc ion.
(3) Asp273 acts as a general acid to protonate the leaving amine group, leading to the collapse of the tetrahedral intermediate and completion of the reaction.

createdupdated
2008-05-132011-12-09


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