DB code: D00673

RLCP classification 1.13.7630.541 : 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 D00675 D00801 D00873 M00030 M00225 M00226
2.30.40.10 : Urease, subunit C; domain 1 D00675 D00801 D00873 M00030 M00225 M00226

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq MEROPS Pfam
O34450 N-acetylglucosamine-6-phosphate deacetylase
EC 3.5.1.25
GlcNAc 6-P deacetylase
NP_391381.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
M38.983 (Metallo)
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
O34450 NAGA_BACSU 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 C00023 C00357 C00001 C00352 C00033
E.C.
Compound Iron N-acetyl-D-glucosamine 6-phosphate H2O D-glucosamine 6-phosphate acetate
Type heavy metal amide group,carbohydrate,phosphate group/phosphate ion H2O amine group,carbohydrate,phosphate group/phosphate ion carboxyl group
ChEBI 18248
82664
15784
15377
47987
15366
PubChem 23925
440996
22247451
962
440997
176
21980959
1un7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1un7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2vhlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2vhlB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1un7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_FE Unbound Bound:GLP Unbound
1un7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_FE Unbound Bound:GLP Unbound
2vhlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_FE Unbound Bound:GLP Unbound
2vhlB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_FE Unbound Bound:GLP Unbound

Reference for Active-site residues
resource references E.C.
PDB;2vhl & literature [1]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1un7A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1un7B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2vhlA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2vhlB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1un7A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 281 HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)
1un7B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 281 HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)
2vhlA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 281 HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)
2vhlB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 281 HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.4, Fig. 7, p. 2815
[2]
p.6389-6390
[4]
p.7960-7961
[5]
p.7951

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY.
Medline ID
PubMed ID 14557261
Journal J Biol Chem
Year 2004
Volume 279
Pages 2809-16
Authors Vincent F, Yates D, Garman E, Davies GJ, Brannigan JA
Title The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.
Related PDB 1un7 2vhl
Related UniProtKB O34450
[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
This enzyme belongs to amidohydrolase superfamily, which comprises a variety of enzymes that catalyze the hydrolysis of a range of substrates with amide or ester groups (see [2]). These enzymes adopt either a mononuclear or binuclear metal center at the active sites (see [2]).
Although this enzyme adopts a binuclear metal center, its homologous counterpart from E. coli utilizes a mononuclear metal center (D00801 in EzCatDB).
The catalytic reacion of this enzyme proceeds as follows (see [1], [4], [5]):
(1) Asp281 acts as a general base to deprotonate the water molecule, which is bound to the two iron atoms.
(2) The activated water, or hydroxide, makes a nucleophilic attack on the carbonyl carbon of the scissile bond, N-acetyl group.
(3) Iron-1 (bound to His202, His223 and Glu136) stabilizes the carbonyl oxygen in the transition state, and enhances the electrophilicity of the carbon through withdrawal of electrons along the carbonyl bond. On the other hand, Iron-2 (bound to His63, His65, Asp281 and Glu136) stabilizes the hydroxide.
(4) Finally, Asp281 acts as a general acid to protonate the leaving amine group, to complete the reaction.

Created Updated
2008-12-02 2010-01-22