1hxe: Difference between revisions
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[[Image:1hxe.gif|left|200px]] | [[Image:1hxe.gif|left|200px]] | ||
'''SERINE PROTEASE''' | {{Structure | ||
|PDB= 1hxe |SIZE=350|CAPTION= <scene name='initialview01'>1hxe</scene>, resolution 2.1Å | |||
|SITE= <scene name='pdbsite=ACT:Active+Site'>ACT</scene> | |||
|LIGAND= <scene name='pdbligand=RB:RUBIDIUM ION'>RB</scene> | |||
|ACTIVITY= [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] | |||
|GENE= | |||
}} | |||
'''SERINE PROTEASE''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1HXE is a [ | 1HXE is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HXE OCA]. | ||
==Reference== | ==Reference== | ||
The molecular environment of the Na+ binding site of thrombin., Zhang E, Tulinsky A, Biophys Chem. 1997 Jan 31;63(2-3):185-200. PMID:[http:// | The molecular environment of the Na+ binding site of thrombin., Zhang E, Tulinsky A, Biophys Chem. 1997 Jan 31;63(2-3):185-200. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9108691 9108691] | ||
[[Category: Homo sapiens]] | [[Category: Homo sapiens]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: serine protease in blood coagulation]] | [[Category: serine protease in blood coagulation]] | ||
''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 11:42:46 2008'' | ||
Revision as of 12:42, 20 March 2008
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| , resolution 2.1Å | |||||||
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| Sites: | |||||||
| Ligands: | |||||||
| Activity: | Thrombin, with EC number 3.4.21.5 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
SERINE PROTEASE
OverviewOverview
When Na+ binds to thrombin, a conformational change is induced that renders the enzyme kinetically faster and more specific in the activation of fibrinogen. Two Na+ binding sites have here been identified crystallographically by exchanging Na+ with Rb+. One is intermolecular, found on the surface between two symmetry-related thrombin molecules. Since it is not present in thrombin crystal structures having different crystal systems, the other Na+ site is the functionally relevant one. The second site has octahedral coordination with the carbonyl oxygen atoms of Arg221A and Lys224 and four conserved water molecules. It is located near Asp189 of the S1 specificity site in an elongated solvent channel (8 x 18 A) formed by four antiparallel beta-strands between Cys182-Cys191 and Val213-Tyr228. This channel, extending from the active site to the opposite surface of the enzyme, was first noted in the hirudin-thrombin structure and contains about 20 conserved water molecules linked together by a hydrogen bonding network that connects to the main chain of thrombin. Although the antiparallel beta-strand interactions of the functional Na+ binding site are the same in prethrombin2, the loops between the strands are very different, so that Asp189 and Arg221A are not positioned properly for either substrate or Na+ binding in prethrombin2. A water molecule with octahedral coordination has also been identified in factor Xa at the topologically equivalent Na+ site position of thrombin. Since activated protein C shows enhanced activity with monovalant cation binding, the same position is probably utilized by Na+. Since thrombin crystals could not be grown in the absence of Na+, the cation was leached from Na(+)-bound thrombin crystals by diffusion/exchange. Although both Na+ and their coordinating water molecules were removed from the Na+ binding sites, the remainder of the thrombin structure was, unexpectedly, the same. The lack of an allosteric change is most likely attributable to crystal packing effects. Thus, the structure of the slow form remains to be established crystallographically.
DiseaseDisease
Known diseases associated with this structure: Dysprothrombinemia OMIM:[176930], Hyperprothrombinemia OMIM:[176930], Hypoprothrombinemia OMIM:[176930]
About this StructureAbout this Structure
1HXE is a Protein complex structure of sequences from Homo sapiens. Full crystallographic information is available from OCA.
ReferenceReference
The molecular environment of the Na+ binding site of thrombin., Zhang E, Tulinsky A, Biophys Chem. 1997 Jan 31;63(2-3):185-200. PMID:9108691
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