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| CATH domain | Related DB codes (homologues) |
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| 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 |
| KEGG pathways | | MAP code | Pathways |
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| MAP00030 | Pentose phosphate pathway |
| UniProtKB:Accession Number | P46859 |
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| Entry name | GNTK_ECOLI |
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| Activity | ATP + D-gluconate = ADP + 6-phospho-D-gluconate. |
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| Subunit |
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| Subcellular location |
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| Cofactor |
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| References for Catalytic Mechanism | | References | Sections | No. of steps in catalysis |
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| [5] | Fig.6, Fig.7, Fig.8, p.1065-1066 |
| | [6] | Fig.1, p.783-786 |
|
| references | | [1] |
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| PubMed ID | 2223776 |
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| Journal | Biochemistry |
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| Year | 1990 |
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| Volume | 29 |
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| Pages | 7451-9 |
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| Authors | Reinstein J, Schlichting I, Wittinghofer A |
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| Title | Structurally and catalytically important residues in the phosphate binding loop of adenylate kinase of Escherichia coli. |
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| [2] |
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| PubMed ID | 8703943 |
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| Journal | Biochemistry |
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| Year | 1996 |
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| Volume | 35 |
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| Pages | 9716-27 |
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| Authors | Scheffzek K, Kliche W, Wiesmuller L, Reinstein J |
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| 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. |
|---|
| [3] |
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| PubMed ID | 9562560 |
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| Journal | Structure |
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| Year | 1998 |
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| Volume | 6 |
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| Pages | 413-9 |
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| Authors | Matte A, Tari LW, Delbaere LT |
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| Title | How do kinases transfer phosphoryl groups? |
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| [4] |
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| PubMed ID | 11369852 |
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| Journal | Protein Sci |
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| Year | 2001 |
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| Volume | 10 |
|---|
| Pages | 1137-49 |
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| Authors | Krell T, Maclean J, Boam DJ, Cooper A, Resmini M, Brocklehurst K, Kelly SM, Price NC, Lapthorn AJ, Coggins JR |
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| Title | Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine. |
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| [5] |
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| Comments | X-RAY CRYSTALLOGRAPHY |
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| PubMed ID | 12054802 |
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| Journal | J Mol Biol |
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| Year | 2002 |
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| Volume | 318 |
|---|
| Pages | 1057-69 |
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| Authors | Kraft L, Sprenger GA, Lindqvist Y |
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| Title | Conformational changes during the catalytic cycle of gluconate kinase as revealed by X-ray crystallography. |
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| Related PDB | 1knq,1ko1,1ko4,1ko5,1ko8,1kof |
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| [6] |
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| PubMed ID | 14568537 |
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| Journal | J Mol Biol |
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| Year | 2003 |
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| Volume | 333 |
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| Pages | 781-815 |
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| Authors | Leipe DD, Koonin EV, Aravind L |
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| Title | Evolution and classification of P-loop kinases and related proteins. |
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| [7] |
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| PubMed ID | 18174226 |
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| Journal | Nucleic Acids Res |
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| Year | 2008 |
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| Volume | 36 |
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| Pages | 1247-59 |
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| Authors | Sherrer RL, O'Donoghue P, Soll D |
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| Title | Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation. |
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| 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)
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| created | updated |
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| 2009-02-05 | 2011-12-13 |
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