EzCatDB: S00671
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DB codeS00671
RLCP classification3.103.75410.402 : Transfer
CATH domainDomain 13.40.50.300 : Rossmann foldCatalytic domain
E.C.2.7.1.12

CATH domainRelated DB codes (homologues)
3.40.50.300 : Rossmann foldS00527,S00547,S00548,S00550,S00554,S00555,S00672,S00676,S00680,S00682,S00913,S00914,S00301,S00302,S00303,S00304,S00307,S00308,S00305,S00306,S00309,S00310,S00311,M00114,M00199,D00129,D00130,D00540,M00186

Enzyme Name
UniProtKBKEGG

P46859
Protein nameThermoresistant gluconokinaseGluconokinase
Gluconokinase (phosphorylating)
Gluconate kinase
SynonymsEC 2.7.1.12
Gluconate kinase 2
RefSeqNP_417894.2 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491997.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PfamPF01202 (SKI)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00030Pentose phosphate pathway

UniProtKB:Accession NumberP46859
Entry nameGNTK_ECOLI
ActivityATP + D-gluconate = ADP + 6-phospho-D-gluconate.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00002C00257C00008C00345
CompoundMagnesiumATPD-gluconateADP6-phospho-D-gluconate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,carboxyl groupamine group,nucleotidecarbohydrate,carboxyl group,phosphate group/phosphate ion
ChEBI18420
15422
33198
16761
48928
PubChem888
5957
10690
6022
91493
             
1knqA00UnboundUnboundUnboundUnboundUnbound
1knqB00UnboundUnboundUnboundUnboundUnbound
1ko1A00UnboundUnboundUnboundUnboundUnbound
1ko1B00UnboundUnboundUnboundUnboundUnbound
1ko4A00UnboundUnboundUnboundUnboundUnbound
1ko4B00UnboundUnboundUnboundUnboundUnbound
1ko5A00Bound:_MGBound:ATPUnboundUnboundUnbound
1ko5B00Bound:_MGBound:ATPUnboundUnboundUnbound
1ko8A00Bound:_MGUnboundUnboundUnboundBound:6PG
1ko8B00UnboundUnboundUnboundUnboundBound:6PG
1kofA00Bound:_MGAnalogue:ACPUnboundUnboundUnbound
1kofB00Bound:_MGAnalogue:ACPUnboundUnboundUnbound

Active-site residues
resource
literature [5]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysiscomment
            
1knqA00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 
1knqB00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 
1ko1A00LYS 21;       
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
invisible 122-130
1ko1B00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
invisible 126-129
1ko4A00LYS 21;       
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
invisible 122-129
1ko4B00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
invisible 125-131
1ko5A00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 
1ko5B00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 
1ko8A00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 
1ko8B00LYS 21;       
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
invisible 123-126
1kofA00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 
1kofB00LYS 21;ARG 124
SER 22;ASP 38;ASP 40(Magnesium binding)
GLY 18;SER 19;GLY 20;LYS 21
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]Fig.6, Fig.7, Fig.8, p.1065-1066
[6]Fig.1, p.783-786

references
[1]
PubMed ID2223776
JournalBiochemistry
Year1990
Volume29
Pages7451-9
AuthorsReinstein J, Schlichting I, Wittinghofer A
TitleStructurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli.
[2]
PubMed ID8703943
JournalBiochemistry
Year1996
Volume35
Pages9716-27
AuthorsScheffzek K, Kliche W, Wiesmuller L, Reinstein J
TitleCrystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.
[3]
PubMed ID9562560
JournalStructure
Year1998
Volume6
Pages413-9
AuthorsMatte A, Tari LW, Delbaere LT
TitleHow do kinases transfer phosphoryl groups?
[4]
PubMed ID11369852
JournalProtein Sci
Year2001
Volume10
Pages1137-49
AuthorsKrell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, Kelly SM, Price NC, Lapthorn AJ, Coggins JR
TitleBiochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.
[5]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID12054802
JournalJ Mol Biol
Year2002
Volume318
Pages1057-69
AuthorsKraft L, Sprenger GA, Lindqvist Y
TitleConformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.
Related PDB1knq,1ko1,1ko4,1ko5,1ko8,1kof
[6]
PubMed ID14568537
JournalJ Mol Biol
Year2003
Volume333
Pages781-815
AuthorsLeipe DD, Koonin EV, Aravind L
TitleEvolution and classification of P-loop kinases and related proteins.
[7]
PubMed ID18174226
JournalNucleic Acids Res
Year2008
Volume36
Pages1247-59
AuthorsSherrer RL, O'Donoghue P, Soll D
TitleCharacterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.

comments
This enzyme is homologous to shikimate kinase (S00304 in EzCatDB) and adenylate kinase (S00305 in EzCatDB).
According to the literature [5], the reaction proceeds as follows:
(0) Magnesium ion, which is bound to Ser22, and Asp38 and Asp40 through a water molecule, is bridging beta- and gamma-phosphate groups of ATP. Arg124 interacts with alpha-phoshpate of ATP, whereas Lys21 interacts with beta- and gamma-phosphate groups. Mainchain amide groups of Gly18-Ser19-Gly20-Lys21 interact mainly with beta-phosphate group of ATP.
(1) Gamma-phosphate oxygen acts as a general base to deprotonate the acceptor group, 6-hydroxyl group, of D-gluconate.
(2) The activated 6-hydroxyl oxygen makes a nucleophilic attack on the gamma-phosphate group, leading to the transition-state. The transferred gamma-phosphate group in the transition-state can be stabilized by Lys21 and magnesium ion, whereas leaving alpha- and beta-phosphate groups can be stabilized by mainchain amide groups and Arg124, as well as the magnesium ion.
(3) The transferred gamma-phsohate group may protonate the leaving beta-phosphate group, completing the reaction. (SN2-like reaction)

createdupdated
2009-02-052011-12-13


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