1b4d: Difference between revisions
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|PDB= 1b4d |SIZE=350|CAPTION= <scene name='initialview01'>1b4d</scene>, resolution 2.00Å | |PDB= 1b4d |SIZE=350|CAPTION= <scene name='initialview01'>1b4d</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CRA:1-DEOXY-1-METHOXYCARBAMIDO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE'>CRA</scene>, <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=CRA:1-DEOXY-1-METHOXYCARBAMIDO-BETA-D-GLUCO-2-HEPTULOPYRANOSONAMIDE'>CRA</scene>, <scene name='pdbligand=IMP:INOSINIC+ACID'>IMP</scene>, <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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b4d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4d OCA], [http://www.ebi.ac.uk/pdbsum/1b4d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b4d RCSB]</span> | |||
}} | }} | ||
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[[Category: Watson, K A.]] | [[Category: Watson, K A.]] | ||
[[Category: Zographos, S E.]] | [[Category: Zographos, S E.]] | ||
[[Category: amidocarbamate]] | [[Category: amidocarbamate]] | ||
[[Category: glycogen phosphorylase]] | [[Category: glycogen phosphorylase]] | ||
[[Category: inhibitor binding]] | [[Category: inhibitor binding]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:53:17 2008'' | ||
Revision as of 18:53, 30 March 2008
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| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | Phosphorylase, with EC number 2.4.1.1 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
AMIDOCARBAMATE INHIBITOR OF GLYCOGEN PHOSPHORYLASE
OverviewOverview
The effects of a number of cryoprotectants on the kinetic and structural properties of glycogen phosphorylase b have been investigated. Kinetic studies showed that glycerol, one of the most commonly used cryoprotectants in X-ray crystallographic studies, is a competitive inhibitor with respect to substrate glucose-1-P with an apparent Ki value of 3.8% (v/v). Cryogenic experiments, with the enzyme, have shown that glycerol binds at the catalytic site and competes with glucose analogues that bind at the catalytic site, thus preventing the formation of complexes. This necessitated a change in the conditions for cryoprotection in crystallographic binding experiments with glycogen phosphorylase. It was found that 2-methyl-2,4-pentanediol (MPD), polyethylene glycols (PEGs) of various molecular weights, and dimethyl sulfoxide (DMSO) activated glycogen phosphorylase b to different extents, by stabilizing its most active conformation, while sucrose acted as a noncompetitive inhibitor and ethylene glycol as an uncompetitive inhibitor with respect to glucose-1-P. A parallel experimental investigation by X-ray crystallography showed that, at 100 K, both MPD and DMSO do not bind at the catalytic site, do not induce any significant conformational change on the enzyme molecule, and hence, are more suitable cryoprotectants than glycerol for binding studies with glycogen phosphorylase.
About this StructureAbout this Structure
1B4D is a Single protein structure of sequence from Oryctolagus cuniculus. Full crystallographic information is available from OCA.
ReferenceReference
Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure., Tsitsanou KE, Oikonomakos NG, Zographos SE, Skamnaki VT, Gregoriou M, Watson KA, Johnson LN, Fleet GW, Protein Sci. 1999 Apr;8(4):741-9. PMID:10211820
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