2skc: Difference between revisions

Revision as of 19:49, 21 February 2008

PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH FLUOROPHOSPHATE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE

OverviewOverview

It has been established that phosphate analogues can activate glycogen phosphorylase reconstituted with pyridoxal in place of the natural cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983. Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by kinetic, ultracentrifugation, and X-ray crystallographic experiments. In solution, the catalytically active species of pyridoxal phosphorylase b adopts a conformation that is more R-state-like than that of native phosphorylase b, but an inactive dimeric species of the enzyme can be stabilized by activator phosphite in combination with the T-state inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the structures of the complexes have been refined to give crystallographic R factors of 18.5-19.2%, for data between 8 and 2.4 A resolution. The anions bind tightly at the catalytic site in a similar but not identical position to that occupied by the cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus atoms distance = 1.2 A). The structural results show that the structures of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall similar to the glucose complex of native T-state phosphorylase b. Structural comparisons suggest that the bound anions, in the position observed in the crystal, might have a structural role for effective catalysis.

About this StructureAbout this Structure

2SKC is a Single protein structure of sequence from Oryctolagus cuniculus with , , and as ligands. This structure supersedes the now removed PDB entry 1SKC. Active as Phosphorylase, with EC number 2.4.1.1 Full crystallographic information is available from OCA.

ReferenceReference

Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal., Oikonomakos NG, Zographos SE, Tsitsanou KE, Johnson LN, Acharya KR, Protein Sci. 1996 Dec;5(12):2416-28. PMID:8976550

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-[[Image:2skc.gif|left|200px]]<br /><applet load="2skc" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2skc.gif|left|200px]]<br /><applet load="2skc" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2skc, resolution 2.40&Aring;" />
 '''PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH FLUOROPHOSPHATE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE'''<br />
 ==Overview==
-It has been established that phosphate analogues can activate glycogen, phosphorylase reconstituted with pyridoxal in place of the natural, cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983., Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by, kinetic, ultracentrifugation, and X-ray crystallographic experiments. In, solution, the catalytically active species of pyridoxal phosphorylase b, adopts a conformation that is more R-state-like than that of native, phosphorylase b, but an inactive dimeric species of the enzyme can be, stabilized by activator phosphite in combination with the T-state, inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with, either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with, native-like unit cell dimensions, and the structures of the complexes have, been refined to give crystallographic R factors of 18.5-19.2%, for data, between 8 and 2.4 A resolution. The anions bind tightly at the catalytic, site in a similar but not identical position to that occupied by the, cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus, atoms distance = 1.2 A). The structural results show that the structures, of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall, similar to the glucose complex of native T-state phosphorylase b., Structural comparisons suggest that the bound anions, in the position, observed in the crystal, might have a structural role for effective, catalysis.
+It has been established that phosphate analogues can activate glycogen phosphorylase reconstituted with pyridoxal in place of the natural cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983. Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by kinetic, ultracentrifugation, and X-ray crystallographic experiments. In solution, the catalytically active species of pyridoxal phosphorylase b adopts a conformation that is more R-state-like than that of native phosphorylase b, but an inactive dimeric species of the enzyme can be stabilized by activator phosphite in combination with the T-state inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the structures of the complexes have been refined to give crystallographic R factors of 18.5-19.2%, for data between 8 and 2.4 A resolution. The anions bind tightly at the catalytic site in a similar but not identical position to that occupied by the cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus atoms distance = 1.2 A). The structural results show that the structures of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall similar to the glucose complex of native T-state phosphorylase b. Structural comparisons suggest that the bound anions, in the position observed in the crystal, might have a structural role for effective catalysis.
 ==About this Structure==
-SKC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with GLC, PLP, FPO and IMP as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1SKC. Active as [http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2SKC OCA].
+SKC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with <scene name='pdbligand=GLC:'>GLC</scene>, <scene name='pdbligand=PLP:'>PLP</scene>, <scene name='pdbligand=FPO:'>FPO</scene> and <scene name='pdbligand=IMP:'>IMP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1SKC. Active as [http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2SKC OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Phosphorylase]]
 [[Category: Single protein]]
-[[Category: Acharya, K.R.]]
+[[Category: Acharya, K R.]]
-[[Category: Johnson, L.N.]]
+[[Category: Johnson, L N.]]
-[[Category: Oikonomakos, N.G.]]
+[[Category: Oikonomakos, N G.]]
-[[Category: Tsitsanou, K.E.]]
+[[Category: Tsitsanou, K E.]]
-[[Category: Zographos, S.E.]]
+[[Category: Zographos, S E.]]
 [[Category: FPO]]
 [[Category: GLC]]
@@ Line 28: / Line 28: @@
 [[Category: pyridoxal phosphate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 14:01:56 2007''
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