6gpb
From Proteopedia
(New page: 200px<br /> <applet load="6gpb" size="450" color="white" frame="true" align="right" spinBox="true" caption="6gpb, resolution 2.86Å" /> '''REFINED CRYSTAL STR...) |
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| - | [[Image:6gpb.gif|left|200px]]<br /> | + | [[Image:6gpb.gif|left|200px]]<br /><applet load="6gpb" size="350" color="white" frame="true" align="right" spinBox="true" |
| - | <applet load="6gpb" size=" | + | |
caption="6gpb, resolution 2.86Å" /> | caption="6gpb, resolution 2.86Å" /> | ||
'''REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX'''<br /> | '''REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of phosphorylase b-heptulose 2-phosphate complex | + | The crystal structure of phosphorylase b-heptulose 2-phosphate complex with oligosaccharide and AMP bound has been refined by molecular dynamics and crystallographic least-squares with the program XPLOR. Shifts in atomic positions of up to 4 A from the native enzyme structure were correctly determined by the program without manual intervention. The final crystallographic R value for data between 8 and 2.86 A resolution is 0.201, and the overall root-mean-square difference between the native and complexed structure is 0.58 A for all protein atoms. The results confirm the previous observation that there is a direct hydrogen bond between the phosphate of heptulose 2-phosphate and the pyridoxal phosphate 5'-phosphate group. The close proximity of the two phosphates is stabilized by an arginine residue, Arg569, which shifts from a site buried in the protein to a position where it can make contact with the product phosphate. There is a mutual interchange in position between the arginine and an acidic group, Asp283. These movements represent the first stage of the allosteric response which converts the catalytic site from a low to a high-affinity binding site. Communication of these changes to other sites is prevented in the crystal by the lattice forces, which also form the subunit interface. The constellation of groups in the phosphorylase transition state analogue complex provides a structural basis for understanding the catalytic mechanism in which the cofactor pyridoxal phosphate 5'-phosphate group functions as a general acid to promote attack by the substrate phosphate on the glycosidic bond when the reaction proceeds in the direction of glycogen degradation. In the direction of glycogen synthesis, stereoelectronic effects contribute to the cleavage of the C-1-O-1 bond. In both reactions the substrate phosphate plays a key role in transition state stabilization. The details of the oligosaccharide, maltoheptaose, interactions with the enzyme at the glycogen storage site are also described. |
==About this Structure== | ==About this Structure== | ||
| - | 6GPB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with H2P, PLP and AMP as [http://en.wikipedia.org/wiki/ligands ligands]. The following page contains interesting information on the relation of 6GPB with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb24_1.html Glycogen Phosphorylase]]. 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:// | + | 6GPB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=H2P:'>H2P</scene>, <scene name='pdbligand=PLP:'>PLP</scene> and <scene name='pdbligand=AMP:'>AMP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. The following page contains interesting information on the relation of 6GPB with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb24_1.html Glycogen Phosphorylase]]. 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=6GPB OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Phosphorylase]] | [[Category: Phosphorylase]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Acharya, K | + | [[Category: Acharya, K R.]] |
| - | [[Category: Johnson, L | + | [[Category: Johnson, L N.]] |
[[Category: AMP]] | [[Category: AMP]] | ||
[[Category: H2P]] | [[Category: H2P]] | ||
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[[Category: glycogen phosphorylase]] | [[Category: glycogen phosphorylase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:16:20 2008'' |
Revision as of 17:16, 21 February 2008
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REFINED CRYSTAL STRUCTURE OF THE PHOSPHORYLASE-HEPTULOSE 2-PHOSPHATE-OLIGOSACCHARIDE-AMP COMPLEX
Overview
The crystal structure of phosphorylase b-heptulose 2-phosphate complex with oligosaccharide and AMP bound has been refined by molecular dynamics and crystallographic least-squares with the program XPLOR. Shifts in atomic positions of up to 4 A from the native enzyme structure were correctly determined by the program without manual intervention. The final crystallographic R value for data between 8 and 2.86 A resolution is 0.201, and the overall root-mean-square difference between the native and complexed structure is 0.58 A for all protein atoms. The results confirm the previous observation that there is a direct hydrogen bond between the phosphate of heptulose 2-phosphate and the pyridoxal phosphate 5'-phosphate group. The close proximity of the two phosphates is stabilized by an arginine residue, Arg569, which shifts from a site buried in the protein to a position where it can make contact with the product phosphate. There is a mutual interchange in position between the arginine and an acidic group, Asp283. These movements represent the first stage of the allosteric response which converts the catalytic site from a low to a high-affinity binding site. Communication of these changes to other sites is prevented in the crystal by the lattice forces, which also form the subunit interface. The constellation of groups in the phosphorylase transition state analogue complex provides a structural basis for understanding the catalytic mechanism in which the cofactor pyridoxal phosphate 5'-phosphate group functions as a general acid to promote attack by the substrate phosphate on the glycosidic bond when the reaction proceeds in the direction of glycogen degradation. In the direction of glycogen synthesis, stereoelectronic effects contribute to the cleavage of the C-1-O-1 bond. In both reactions the substrate phosphate plays a key role in transition state stabilization. The details of the oligosaccharide, maltoheptaose, interactions with the enzyme at the glycogen storage site are also described.
About this Structure
6GPB is a Single protein structure of sequence from [1] with , and as ligands. The following page contains interesting information on the relation of 6GPB with [Glycogen Phosphorylase]. Active as Phosphorylase, with EC number 2.4.1.1 Full crystallographic information is available from OCA.
Reference
Refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP complex., Johnson LN, Acharya KR, Jordan MD, McLaughlin PJ, J Mol Biol. 1990 Feb 5;211(3):645-61. PMID:2106586
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