2pgq: Difference between revisions
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New page: left|200px<br /> <applet load="2pgq" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pgq, resolution 1.80Å" /> '''Human thrombin muta... |
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[[Image:2pgq. | [[Image:2pgq.jpg|left|200px]]<br /><applet load="2pgq" size="350" color="white" frame="true" align="right" spinBox="true" | ||
<applet load="2pgq" size=" | |||
caption="2pgq, resolution 1.80Å" /> | caption="2pgq, resolution 1.80Å" /> | ||
'''Human thrombin mutant C191A-C220A in complex with the inhibitor PPACK'''<br /> | '''Human thrombin mutant C191A-C220A in complex with the inhibitor PPACK'''<br /> | ||
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==Overview== | ==Overview== | ||
Na(+) binding near the primary specificity pocket of thrombin promotes the, procoagulant, prothrombotic, and signaling functions of the enzyme. The, effect is mediated allosterically by a communication between the Na(+), site and regions involved in substrate recognition. Using a panel of 78, Ala mutants of thrombin, we have mapped the allosteric core of residues, that are energetically linked to Na(+) binding. These residues are, Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the, bound Na(+). Among these residues, Asp-189 shares with Asp-221 the, important function of transducing Na(+) binding into enhanced catalytic, activity. None of the residues of exosite I, exosite II, or the 60-loop, plays a significant role in Na(+) binding and allosteric transduction., X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast), forms of thrombin, free or bound to the active site inhibitor, H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes, induced by Na(+) binding. The slow --> fast transition results in, formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189, and Ser-195 for substrate binding, and a significant shift of the side, chain of Glu-192 linked to a rearrangement of the network of water, molecules that connect the bound Na(+) to Ser-195 in the active site. The, changes in the water network and the allosteric core explain the, thermodynamic signatures linked to Na(+) binding and the mechanism of, thrombin activation by Na(+). The role of the water network uncovered in, this study establishes a new paradigm for the allosteric regulation of, thrombin and other Na(+)-activated enzymes involved in blood coagulation, and the immune response. | Na(+) binding near the primary specificity pocket of thrombin promotes the, procoagulant, prothrombotic, and signaling functions of the enzyme. The, effect is mediated allosterically by a communication between the Na(+), site and regions involved in substrate recognition. Using a panel of 78, Ala mutants of thrombin, we have mapped the allosteric core of residues, that are energetically linked to Na(+) binding. These residues are, Asp-189, Glu-217, Asp-222, and Tyr-225, all in close proximity to the, bound Na(+). Among these residues, Asp-189 shares with Asp-221 the, important function of transducing Na(+) binding into enhanced catalytic, activity. None of the residues of exosite I, exosite II, or the 60-loop, plays a significant role in Na(+) binding and allosteric transduction., X-ray crystal structures of the Na(+)-free (slow) and Na(+)-bound (fast), forms of thrombin, free or bound to the active site inhibitor, H-d-Phe-Pro-Arg-chloromethyl-ketone, document the conformational changes, induced by Na(+) binding. The slow --> fast transition results in, formation of the Arg-187:Asp-222 ion pair, optimal orientation of Asp-189, and Ser-195 for substrate binding, and a significant shift of the side, chain of Glu-192 linked to a rearrangement of the network of water, molecules that connect the bound Na(+) to Ser-195 in the active site. The, changes in the water network and the allosteric core explain the, thermodynamic signatures linked to Na(+) binding and the mechanism of, thrombin activation by Na(+). The role of the water network uncovered in, this study establishes a new paradigm for the allosteric regulation of, thrombin and other Na(+)-activated enzymes involved in blood coagulation, and the immune response. | ||
==About this Structure== | ==About this Structure== | ||
2PGQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with NAG and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] Full crystallographic information is available from [http:// | 2PGQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=NAG:'>NAG</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Thrombin Thrombin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.5 3.4.21.5] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PGQ OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: serine protease]] | [[Category: serine protease]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:32:33 2008'' | ||
