DB code: S00671

RLCP classification 3.103.75410.402 : Transfer
CATH domain 3.40.50.300 : Rossmann fold Catalytic domain
E.C. 2.7.1.12
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.300 : Rossmann fold S00527 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P46859 Thermoresistant gluconokinase
EC 2.7.1.12
Gluconate kinase 2
NP_417894.2 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491997.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01202 (SKI)
[Graphical View]

KEGG enzyme name
Gluconokinase
Gluconokinase (phosphorylating)
Gluconate kinase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P46859 GNTK_ECOLI ATP + D-gluconate = ADP + 6-phospho-D-gluconate.

KEGG Pathways
Map code Pathways E.C.
MAP00030 Pentose phosphate pathway

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00257 C00008 C00345
E.C.
Compound Magnesium ATP D-gluconate ADP 6-phospho-D-gluconate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,carboxyl group amine group,nucleotide carbohydrate,carboxyl group,phosphate group/phosphate ion
ChEBI 18420
15422
33198
16761
48928
PubChem 888
5957
10690
6022
91493
1knqA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1knqB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ko1A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ko1B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ko4A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ko4B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1ko5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:ATP Unbound Unbound Unbound
1ko5B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Bound:ATP Unbound Unbound Unbound
1ko8A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Unbound Unbound Unbound Bound:6PG
1ko8B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:6PG
1kofA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:ACP Unbound Unbound Unbound
1kofB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:ACP Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1knqA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21
1knqB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21
1ko1A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21; SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21 invisible 122-130
1ko1B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21 invisible 126-129
1ko4A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21; SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21 invisible 122-129
1ko4B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21 invisible 125-131
1ko5A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21
1ko5B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21
1ko8A00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21
1ko8B00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21; SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21 invisible 123-126
1kofA00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21
1kofB00 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 21;ARG 124 SER 22;ASP 38;ASP 40(Magnesium binding) GLY 18;SER 19;GLY 20;LYS 21

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
Fig.6, Fig.7, Fig.8, p.1065-1066
[6]
Fig.1, p.783-786

References
[1]
Resource
Comments
Medline ID
PubMed ID 2223776
Journal Biochemistry
Year 1990
Volume 29
Pages 7451-9
Authors Reinstein J, Schlichting I, Wittinghofer A
Title Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8703943
Journal Biochemistry
Year 1996
Volume 35
Pages 9716-27
Authors Scheffzek K, Kliche W, Wiesmuller L, Reinstein J
Title Crystal 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.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9562560
Journal Structure
Year 1998
Volume 6
Pages 413-9
Authors Matte A, Tari LW, Delbaere LT
Title How do kinases transfer phosphoryl groups?
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 11369852
Journal Protein Sci
Year 2001
Volume 10
Pages 1137-49
Authors Krell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, Kelly SM, Price NC, Lapthorn AJ, Coggins JR
Title Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 12054802
Journal J Mol Biol
Year 2002
Volume 318
Pages 1057-69
Authors Kraft L, Sprenger GA, Lindqvist Y
Title Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography.
Related PDB 1knq 1ko1 1ko4 1ko5 1ko8 1kof
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 14568537
Journal J Mol Biol
Year 2003
Volume 333
Pages 781-815
Authors Leipe DD, Koonin EV, Aravind L
Title Evolution and classification of P-loop kinases and related proteins.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 18174226
Journal Nucleic Acids Res
Year 2008
Volume 36
Pages 1247-59
Authors Sherrer RL, O'Donoghue P, Soll D
Title Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation.
Related PDB
Related UniProtKB

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)

Created Updated
2009-02-05 2011-12-13