EzCatDB: D00673
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DB codeD00673
RLCP classification1.13.7630.541 : 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 1D00675,D00801,D00873,M00030,M00225,M00226
3.20.20.140 : TIM BarrelS00231,S00232,M00186,D00675,D00801,D00873,M00030,M00225,M00226

Enzyme Name
UniProtKBKEGG

O34450
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_391381.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
MEROPSM38.983 (Metallo)
PfamPF01979 (Amidohydro_1)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00530Aminosugars metabolism

UniProtKB:Accession NumberO34450
Entry nameNAGA_BACSU
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

CofactorsSubstratesProducts
KEGG-idC00023C00357C00001C00352C00033
CompoundIronN-acetyl-D-glucosamine 6-phosphateH2OD-glucosamine 6-phosphateacetate
Typeheavy metalamide group,carbohydrate,phosphate group/phosphate ionH2Oamine group,carbohydrate,phosphate group/phosphate ioncarboxyl group
ChEBI18248
82664
15784
15377
47987
15366
PubChem23925
440996
962
22247451
440997
21980959
176
             
1un7A01UnboundUnbound UnboundUnbound
1un7B01UnboundUnbound UnboundUnbound
2vhlA01UnboundUnbound UnboundUnbound
2vhlB01UnboundUnbound UnboundUnbound
1un7A02Bound:2x_FEUnbound Bound:GLPUnbound
1un7B02Bound:2x_FEUnbound Bound:GLPUnbound
2vhlA02Bound:2x_FEUnbound Bound:GLPUnbound
2vhlB02Bound:2x_FEUnbound Bound:GLPUnbound

Active-site residues
resource
PDB;2vhl & literature [1]
pdbCatalytic residuesCofactor-binding residues
          
1un7A01 
 
1un7B01 
 
2vhlA01 
 
2vhlB01 
 
1un7A02ASP 281
HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)
1un7B02ASP 281
HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)
2vhlA02ASP 281
HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)
2vhlB02ASP 281
HIS 202;HIS 223(Iron-1);GLU 136(Iron-1 & 2);HIS 63;HIS 65;ASP 281(Iron-2)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.4, Fig. 7, p. 2815
[2]p.6389-6390
[4]p.7960-7961
[5]p.7951

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY.
PubMed ID14557261
JournalJ Biol Chem
Year2004
Volume279
Pages2809-16
AuthorsVincent F, Yates D, Garman E, Davies GJ, Brannigan JA
TitleThe three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.
Related PDB1un7,2vhl
Related UniProtKBO34450
[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, 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.

createdupdated
2008-12-022010-01-22


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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