2pgb
From Proteopedia
(New page: 200px<br /> <applet load="2pgb" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pgb, resolution 1.54Å" /> '''Inhibitor-free huma...) |
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caption="2pgb, resolution 1.54Å" /> | caption="2pgb, resolution 1.54Å" /> | ||
'''Inhibitor-free human thrombin mutant C191A-C220A'''<br /> | '''Inhibitor-free human thrombin mutant C191A-C220A'''<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. | ||
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| - | ==Disease== | ||
| - | Known diseases associated with this structure: Dysprothrombinemia OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176930 176930]], Hyperprothrombinemia OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176930 176930]], Hypoprothrombinemia OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176930 176930]] | ||
==About this Structure== | ==About this Structure== | ||
| - | 2PGB 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 SO4 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:// | + | 2PGB 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=SO4:'>SO4</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=2PGB 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 14:32:30 2008'' |
Revision as of 12:32, 23 January 2008
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Inhibitor-free human thrombin mutant C191A-C220A
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.
About this Structure
2PGB is a Protein complex structure of sequences from Homo sapiens with and as ligands. Active as Thrombin, with EC number 3.4.21.5 Full crystallographic information is available from OCA.
Reference
Molecular dissection of Na+ binding to thrombin., Pineda AO, Carrell CJ, Bush LA, Prasad S, Caccia S, Chen ZW, Mathews FS, Di Cera E, J Biol Chem. 2004 Jul 23;279(30):31842-53. Epub 2004 May 19. PMID:15152000
Page seeded by OCA on Wed Jan 23 14:32:30 2008
Categories: Homo sapiens | Protein complex | Thrombin | Bush-Pelc, L.A. | Cera, E.Di. | Chen, Z. | Marino, F. | Mathews, F.S. | Pineda, A.O. | NAG | SO4 | Serine protease
