2pri: Difference between revisions
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'''BINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B''' | {{Structure | ||
|PDB= 2pri |SIZE=350|CAPTION= <scene name='initialview01'>2pri</scene>, resolution 2.30Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=D6G:2-DEOXY-GLUCOSE-6-PHOSPHATE'>D6G</scene> and <scene name='pdbligand=PLP:PYRIDOXAL-5'-PHOSPHATE'>PLP</scene> | |||
|ACTIVITY= [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] | |||
|GENE= | |||
}} | |||
'''BINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2PRI is a [ | 2PRI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. This structure supersedes the now removed PDB entry 1PRI. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PRI OCA]. | ||
==Reference== | ==Reference== | ||
The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies., Oikonomakos NG, Zographos SE, Johnson LN, Papageorgiou AC, Acharya KR, J Mol Biol. 1995 Dec 15;254(5):900-17. PMID:[http:// | The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies., Oikonomakos NG, Zographos SE, Johnson LN, Papageorgiou AC, Acharya KR, J Mol Biol. 1995 Dec 15;254(5):900-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7500360 7500360] | ||
[[Category: Oryctolagus cuniculus]] | [[Category: Oryctolagus cuniculus]] | ||
[[Category: Phosphorylase]] | [[Category: Phosphorylase]] | ||
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[[Category: glycogen phosphorylase]] | [[Category: glycogen phosphorylase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:16:32 2008'' | ||
Revision as of 16:16, 20 March 2008
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| 2pri, resolution 2.30Å | |||||||||||||
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| Ligands: | D6G and PLP | ||||||||||||
| Activity: | Phosphorylase, with EC number 2.4.1.1 | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
BINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B
Overview
Kinetic and crystallographic studies have characterized the effect of 2-deoxy-glucose 6-phosphate on the catalytic and structural properties of glycogen phosphorylase b. Previous work on the binding of glucose 6-phosphate, a potent physiological inhibitor of the enzyme, to T state phosphorylase b in the crystal showed that the inhibitor binds at the allosteric site and induces substantial conformational changes that affect the subunit-subunit interface. The hydrogen-bond from the O-2 hydroxyl of glucose 6-phosphate to the main-chain oxygen of Val40' represents the only hydrogen bond from the sugar to the other subunit, and this interaction appears important for promoting a more "tensed" structure than native T state phosphorylase b. 2-Deoxy-glucose 6-phosphate acts competitively with both the activator AMP and the substrate glucose 1-phosphate, with Ki values of 0.53 mM and 1.23 mM, respectively. The binding of 2-deoxy-glucose 6-phosphate to T state glycogen phosphorylase b in the crystal, has been investigated and the complex phosphorylase b: 2-deoxy-glucose 6-phosphate has been refined to give a crystallographic R factor of 17.3%, for data between 8 A and 2.3 A. 2-Deoxy-glucose 6-phosphate binds at the allosteric site as the a anomer and adopts a different conformation compared to glucose 6-phosphate. The two conformations differ by 160 degrees in the torsion angle about the C-5-C-6 bond. The contacts from the phosphate group are essentially identical to those made by the phosphate of glucose 6-phosphate but the 2-deoxy glucosyl moiety binds in a quite different orientation compared to the glucosyl of glucose 6-phosphate. 2-Deoxy-glucose 6-phosphate can be accommodated in the allosteric site with very little change in the protein, while structural comparisons show that the phosphorylase b: 2-deoxy-glucose 6-phosphate complex structure is overall more similar to a glucose-like complex than to the Glc-6-P complex structure.
About this Structure
2PRI is a Single protein structure of sequence from Oryctolagus cuniculus. This structure supersedes the now removed PDB entry 1PRI. Full crystallographic information is available from OCA.
Reference
The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies., Oikonomakos NG, Zographos SE, Johnson LN, Papageorgiou AC, Acharya KR, J Mol Biol. 1995 Dec 15;254(5):900-17. PMID:7500360
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