DB code: D00801

RLCP classification 1.13.7495.453 : Hydrolysis
CATH domain 2.30.40.10 : Urease, subunit C; domain 1
3.20.20.140 : TIM Barrel Catalytic domain
E.C. 3.5.1.25
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.20.20.140 : TIM Barrel S00231 S00232 M00186 D00673 D00675 D00873 M00030 M00225 M00226
2.30.40.10 : Urease, subunit C; domain 1 D00673 D00675 D00873 M00030 M00225 M00226

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P0AF18 N-acetylglucosamine-6-phosphate deacetylase
EC 3.5.1.25
GlcNAc 6-P deacetylase
NP_415203.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488957.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01979 (Amidohydro_1)
[Graphical View]

KEGG enzyme name
N-Acetylglucosamine-6-phosphate deacetylase
Acetylglucosamine phosphate deacetylase
Acetylaminodeoxyglucosephosphate acetylhydrolase
2-Acetamido-2-deoxy-D-glucose-6-phosphate amidohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P0AF18 NAGA_ECOLI N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate.

KEGG Pathways
Map code Pathways E.C.
MAP00530 Aminosugars metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00357 C00001 C00352 C00033 I00110
E.C.
Compound Zinc N-acetyl-D-glucosamine 6-phosphate H2O D-glucosamine 6-phosphate acetate N-tetrahedral intermediate of N-acetyl-D-glucosamine 6-phosphate
Type heavy metal amide group,carbohydrate,phosphate group/phosphate ion H2O amine group,carbohydrate,phosphate group/phosphate ion carboxyl group
ChEBI 29105
15784
15377
47987
15366
PubChem 32051
440996
22247451
962
440997
176
21980959
1ymyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ymyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1yrrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1yrrB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p50A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p50B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p50C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p50D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p53A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p53B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ymyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ymyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1yrrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1yrrB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2p50A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
2p50B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
2p50C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
2p50D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
2p53A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Transition-state-analogue:NNG
2p53B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Transition-state-analogue:NNG

Reference for Active-site residues
resource references E.C.
2p50, 2p53 & literature [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ymyA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ymyB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1yrrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1yrrB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2p50A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2p50B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2p50C01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2p50D01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2p53A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2p53B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ymyA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding) invisible 139-144
1ymyB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding) invisible 138-152
1yrrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding) invisible 141
1yrrB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding) invisible 137-152
2p50A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding)
2p50B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding)
2p50C02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding)
2p50D02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143;ASP 273 GLU 131;HIS 195;HIS 216(Zinc binding)
2p53A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143; GLU 131;HIS 195;HIS 216(Zinc binding) mutant D273N
2p53B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 143; GLU 131;HIS 195;HIS 216(Zinc binding) mutant D273N

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p. 317
[5]
Fig.5, p.7951

References
[1]
Resource
Comments
Medline ID
PubMed ID 9143339
Journal Arch Biochem Biophys
Year 1997
Volume 340
Pages 338-46
Authors Souza JM, Plumbridge JA, Calcagno ML
Title N-acetylglucosamine-6-phosphate deacetylase from Escherichia coli: purification and molecular and kinetic characterization.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 15850372
Journal Biochemistry
Year 2005
Volume 44
Pages 6383-91
Authors Seibert CM, Raushel FM
Title Structural and catalytic diversity within the amidohydrolase superfamily.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 16630633
Journal J Mol Biol
Year 2006
Volume 359
Pages 308-21
Authors Ferreira FM, Mendoza-Hernandez G, Castaneda-Bueno M, Aparicio R, Fischer H, Calcagno ML, Oliva G
Title Structural analysis of N-acetylglucosamine-6-phosphate deacetylase apoenzyme from Escherichia coli.
Related PDB 1yrr
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 17567048
Journal Biochemistry
Year 2007
Volume 46
Pages 7953-62
Authors Hall RS, Brown S, Fedorov AA, Fedorov EV, Xu C, Babbitt PC, Almo SC, Raushel FM
Title Structural diversity within the mononuclear and binuclear active sites of N-acetyl-D-glucosamine-6-phosphate deacetylase.
Related PDB 2p50 2p53
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 17567047
Journal Biochemistry
Year 2007
Volume 46
Pages 7942-52
Authors Hall RS, Xiang DF, Xu C, Raushel FM
Title N-Acetyl-D-glucosamine-6-phosphate deacetylase: substrate activation via a single divalent metal ion.
Related PDB
Related UniProtKB

Comments
(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.
This enzyme belongs to amidohydrolase superfamily.
According to the literature [4] and [5], the reaction proceeds as follows:

Created Updated
2008-05-13 2011-12-09