2rk7: Difference between revisions

Revision as of 19:48, 21 February 2008

The Structure of rat cytosolic PEPCK in complex with oxalate

OverviewOverview

The mechanisms of molecular recognition of phosphoenolpyruvate (PEP) and oxaloacetate (OAA) by cytosolic phosphoenolpyruvate carboxykinase (cPEPCK) were investigated by the systematic evaluation of a variety of PEP and OAA analogues as potential reversible inhibitors of the enzyme against PEP. The molecules that inhibit the enzyme in a competitive fashion were found to fall into two general classes. Those molecules that mimic the binding geometry of PEP, namely phosphoglycolate and 3-phosphonopropionate, are found to bind weakly (millimolar Ki values). In contrast, those competitive inhibitors that mimic the binding of OAA (oxalate and phosphonoformate) coordinate directly to the active site manganese ion and bind an order of magnitude more tightly (micromolar Ki values). The competitive inhibitor sulfoacetate is found to be an outlier of these two classes, binding in a hybrid fashion utilizing modes of recognition of both PEP and OAA in order to achieve a micromolar inhibition constant in the absence of direct coordination to the active site metal. The kinetic studies in combination with the structural characterization of the five aforementioned competitive inhibitors demonstrate the molecular requirements for high affinity binding of molecules to the active site of the enzyme. These features include cis-planar carbonyl groups that are required for coordination to the active site metal, a bridging electron rich atom at the position corresponding to the C2 methylene group of OAA to facilitate interactions with R405, a carboxylate or sulfonate moiety at a position corresponding to the C1 carboxylate of OAA, and the edge-on aromatic interaction between a carboxylate and Y235.

About this StructureAbout this Structure

2RK7 is a Single protein structure of sequence from Rattus norvegicus with , and as ligands. Active as Phosphoenolpyruvate carboxykinase (GTP), with EC number 4.1.1.32 Known structural/functional Sites: , , , , , , and . Full crystallographic information is available from OCA.

ReferenceReference

Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition., Stiffin RM, Sullivan SM, Carlson GM, Holyoak T, Biochemistry. 2008 Feb 19;47(7):2099-109. Epub 2008 Jan 16. PMID:18197707

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 ==Overview==
-The mechanisms of molecular recognition of phosphoenolpyruvate (PEP) and, oxaloacetate (OAA) by cytosolic phosphoenolpyruvate carboxykinase (cPEPCK), were investigated by the systematic evaluation of a variety of PEP and OAA, analogues as potential reversible inhibitors of the enzyme against PEP., The molecules that inhibit the enzyme in a competitive fashion were found, to fall into two general classes. Those molecules that mimic the binding, geometry of PEP, namely phosphoglycolate and 3-phosphonopropionate, are, found to bind weakly (millimolar Ki values). In contrast, those, competitive inhibitors that mimic the binding of OAA (oxalate and, phosphonoformate) coordinate directly to the active site manganese ion and, bind an order of magnitude more tightly (micromolar Ki values). The, competitive inhibitor sulfoacetate is found to be an outlier of these two, classes, binding in a hybrid fashion utilizing modes of recognition of, both PEP and OAA in order to achieve a micromolar inhibition constant in, the absence of direct coordination to the active site metal. The kinetic, studies in combination with the structural characterization of the five, aforementioned competitive inhibitors demonstrate the molecular, requirements for high affinity binding of molecules to the active site of, the enzyme. These features include cis-planar carbonyl groups that are, required for coordination to the active site metal, a bridging electron, rich atom at the position corresponding to the C2 methylene group of OAA, to facilitate interactions with R405, a carboxylate or sulfonate moiety at, a position corresponding to the C1 carboxylate of OAA, and the edge-on, aromatic interaction between a carboxylate and Y235.
+The mechanisms of molecular recognition of phosphoenolpyruvate (PEP) and oxaloacetate (OAA) by cytosolic phosphoenolpyruvate carboxykinase (cPEPCK) were investigated by the systematic evaluation of a variety of PEP and OAA analogues as potential reversible inhibitors of the enzyme against PEP. The molecules that inhibit the enzyme in a competitive fashion were found to fall into two general classes. Those molecules that mimic the binding geometry of PEP, namely phosphoglycolate and 3-phosphonopropionate, are found to bind weakly (millimolar Ki values). In contrast, those competitive inhibitors that mimic the binding of OAA (oxalate and phosphonoformate) coordinate directly to the active site manganese ion and bind an order of magnitude more tightly (micromolar Ki values). The competitive inhibitor sulfoacetate is found to be an outlier of these two classes, binding in a hybrid fashion utilizing modes of recognition of both PEP and OAA in order to achieve a micromolar inhibition constant in the absence of direct coordination to the active site metal. The kinetic studies in combination with the structural characterization of the five aforementioned competitive inhibitors demonstrate the molecular requirements for high affinity binding of molecules to the active site of the enzyme. These features include cis-planar carbonyl groups that are required for coordination to the active site metal, a bridging electron rich atom at the position corresponding to the C2 methylene group of OAA to facilitate interactions with R405, a carboxylate or sulfonate moiety at a position corresponding to the C1 carboxylate of OAA, and the edge-on aromatic interaction between a carboxylate and Y235.
 ==About this Structure==
-RK7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=OXL:'>OXL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] Known structural/functional Sites: <scene name='pdbsite=AC1:Mn Binding Site For Residue A 700'>AC1</scene>, <scene name='pdbsite=AC2:Na Binding Site For Residue A 701'>AC2</scene>, <scene name='pdbsite=AC3:Mn Binding Site For Residue B 700'>AC3</scene>, <scene name='pdbsite=AC4:Na Binding Site For Residue B 701'>AC4</scene>, <scene name='pdbsite=AC5:Oxl Binding Site For Residue A 5575'>AC5</scene>, <scene name='pdbsite=AC6:Oxl Binding Site For Residue B 5575'>AC6</scene>, <scene name='pdbsite=AC7:Mn Binding Site For Residue B 5576'>AC7</scene> and <scene name='pdbsite=AC8:Mn Binding Site For Residue A 5576'>AC8</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RK7 OCA].
+RK7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=MN:'>MN</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=OXL:'>OXL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphoenolpyruvate_carboxykinase_(GTP) Phosphoenolpyruvate carboxykinase (GTP)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.32 4.1.1.32] Known structural/functional Sites: <scene name='pdbsite=AC1:Mn+Binding+Site+For+Residue+A+700'>AC1</scene>, <scene name='pdbsite=AC2:Na+Binding+Site+For+Residue+A+701'>AC2</scene>, <scene name='pdbsite=AC3:Mn+Binding+Site+For+Residue+B+700'>AC3</scene>, <scene name='pdbsite=AC4:Na+Binding+Site+For+Residue+B+701'>AC4</scene>, <scene name='pdbsite=AC5:Oxl+Binding+Site+For+Residue+A+5575'>AC5</scene>, <scene name='pdbsite=AC6:Oxl+Binding+Site+For+Residue+B+5575'>AC6</scene>, <scene name='pdbsite=AC7:Mn+Binding+Site+For+Residue+B+5576'>AC7</scene> and <scene name='pdbsite=AC8:Mn+Binding+Site+For+Residue+A+5576'>AC8</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RK7 OCA].
 ==Reference==
-Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition., Stiffin RM, Sullivan SM, Carlson GM, Holyoak T, Biochemistry. 2008 Jan 16;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18197707 18197707]
+Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition., Stiffin RM, Sullivan SM, Carlson GM, Holyoak T, Biochemistry. 2008 Feb 19;47(7):2099-109. Epub 2008 Jan 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18197707 18197707]
 [[Category: Phosphoenolpyruvate carboxykinase (GTP)]]
 [[Category: Rattus norvegicus]]
 [[Category: Single protein]]
-[[Category: Carlson, G.M.]]
+[[Category: Carlson, G M.]]
 [[Category: Holyoak, T.]]
-[[Category: Stiffin, R.M.]]
+[[Category: Stiffin, R M.]]
-[[Category: Sullivan, S.M.]]
+[[Category: Sullivan, S M.]]
 [[Category: MN]]
 [[Category: NA]]
@@ Line 29: / Line 29: @@
 [[Category: nucleotide-binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 31 11:00:42 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:48:01 2008''