Crystal Structure of Human α-Thrombin Complexed with Hirugen and p-Amidinophenylpyruvate at 1.6 Å Resolution
Crystals of human α-thrombin complexed with hirugen and the α-keto acid thrombin inhibitor APPA ( p-amidinophenylpyruvate) that diffract to 1.6 Å resolution were obtained by soaking an α-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier...
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| Veröffentlicht in: | Archives of biochemistry and biophysics 1995-09, Vol.322 (1), p.198-203 |
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| creator | Chen, Z.G. Li, Y. Mulichak, A.M. Lewis, S.D. Shafer, J.A. |
| description | Crystals of human α-thrombin complexed with hirugen and the α-keto acid thrombin inhibitor APPA (
p-amidinophenylpyruvate) that diffract to 1.6 Å resolution were obtained by soaking an α-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an
R factor of 18.7% at 1.6 Å resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with Oγ of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin. |
| doi_str_mv | 10.1006/abbi.1995.1452 |
| format | Article |
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p-amidinophenylpyruvate) that diffract to 1.6 Å resolution were obtained by soaking an α-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an
R factor of 18.7% at 1.6 Å resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with Oγ of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.</description><identifier>ISSN: 0003-9861</identifier><identifier>EISSN: 1096-0384</identifier><identifier>DOI: 10.1006/abbi.1995.1452</identifier><identifier>PMID: 7574675</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Amino Acid Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hirudins - analogs & derivatives ; Hirudins - chemistry ; Hirudins - genetics ; Humans ; Hydrogen Bonding ; In Vitro Techniques ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Peptide Fragments - chemistry ; Peptide Fragments - genetics ; Phenylpyruvic Acids - chemistry ; Protein Conformation ; Thrombin - chemistry ; Thrombin - genetics ; Trypsin - chemistry</subject><ispartof>Archives of biochemistry and biophysics, 1995-09, Vol.322 (1), p.198-203</ispartof><rights>1995 Academic Press</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c254t-2827395cbd3789fcad648911d67ef9a299732263424561c1e3f4bfaa6a6ca0483</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1006/abbi.1995.1452$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/7574675$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Z.G.</creatorcontrib><creatorcontrib>Li, Y.</creatorcontrib><creatorcontrib>Mulichak, A.M.</creatorcontrib><creatorcontrib>Lewis, S.D.</creatorcontrib><creatorcontrib>Shafer, J.A.</creatorcontrib><title>Crystal Structure of Human α-Thrombin Complexed with Hirugen and p-Amidinophenylpyruvate at 1.6 Å Resolution</title><title>Archives of biochemistry and biophysics</title><addtitle>Arch Biochem Biophys</addtitle><description>Crystals of human α-thrombin complexed with hirugen and the α-keto acid thrombin inhibitor APPA (
p-amidinophenylpyruvate) that diffract to 1.6 Å resolution were obtained by soaking an α-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an
R factor of 18.7% at 1.6 Å resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with Oγ of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.</description><subject>Amino Acid Sequence</subject><subject>Binding Sites</subject><subject>Crystallization</subject><subject>Crystallography, X-Ray</subject><subject>Hirudins - analogs & derivatives</subject><subject>Hirudins - chemistry</subject><subject>Hirudins - genetics</subject><subject>Humans</subject><subject>Hydrogen Bonding</subject><subject>In Vitro Techniques</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Molecular Structure</subject><subject>Peptide Fragments - chemistry</subject><subject>Peptide Fragments - genetics</subject><subject>Phenylpyruvic Acids - chemistry</subject><subject>Protein Conformation</subject><subject>Thrombin - chemistry</subject><subject>Thrombin - genetics</subject><subject>Trypsin - chemistry</subject><issn>0003-9861</issn><issn>1096-0384</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1995</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kM1u1DAUhS1EVYbClh2SV-wS7Nhx4mU1gg5SJSQoa8uxbxijxA7-aZkH6APxDOz7TEw0I3as7uKc80n3Q-gNJTUlRLzXw-BqKmVbU942z9CGEikqwnr-HG0IIaySvaAv0MuUfhBCKRfNJbrs2o6Lrt0gv42HlPWEv-ZYTC4RcBjxrsza46ff1d0-hnlwHm_DvEzwCyx-cHmPdy6W7-Cx9hYv1fXsrPNh2YM_TMshlnudAeuMaS3wn0f8BVKYSnbBv0IXo54SvD7fK_Tt44e77a66_XzzaXt9W5mm5blq-qZjsjWDZV0vR6Ot4L2k1IoORqkbKTvWNILxhreCGgps5MOotdDCaMJ7doXenbhLDD8LpKxmlwxMk_YQSlJd1x7nbC3Wp6KJIaUIo1qim3U8KErUKlitgtUqWK2Cj4O3Z3IZZrD_6mejx7w_5XB8795BVMk48Aasi2CyssH9D_0XpHeLgA</recordid><startdate>19950910</startdate><enddate>19950910</enddate><creator>Chen, Z.G.</creator><creator>Li, Y.</creator><creator>Mulichak, A.M.</creator><creator>Lewis, S.D.</creator><creator>Shafer, J.A.</creator><general>Elsevier Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>19950910</creationdate><title>Crystal Structure of Human α-Thrombin Complexed with Hirugen and p-Amidinophenylpyruvate at 1.6 Å Resolution</title><author>Chen, Z.G. ; Li, Y. ; Mulichak, A.M. ; Lewis, S.D. ; Shafer, J.A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c254t-2827395cbd3789fcad648911d67ef9a299732263424561c1e3f4bfaa6a6ca0483</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1995</creationdate><topic>Amino Acid Sequence</topic><topic>Binding Sites</topic><topic>Crystallization</topic><topic>Crystallography, X-Ray</topic><topic>Hirudins - analogs & derivatives</topic><topic>Hirudins - chemistry</topic><topic>Hirudins - genetics</topic><topic>Humans</topic><topic>Hydrogen Bonding</topic><topic>In Vitro Techniques</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Molecular Structure</topic><topic>Peptide Fragments - chemistry</topic><topic>Peptide Fragments - genetics</topic><topic>Phenylpyruvic Acids - chemistry</topic><topic>Protein Conformation</topic><topic>Thrombin - chemistry</topic><topic>Thrombin - genetics</topic><topic>Trypsin - chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chen, Z.G.</creatorcontrib><creatorcontrib>Li, Y.</creatorcontrib><creatorcontrib>Mulichak, A.M.</creatorcontrib><creatorcontrib>Lewis, S.D.</creatorcontrib><creatorcontrib>Shafer, J.A.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Archives of biochemistry and biophysics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Z.G.</au><au>Li, Y.</au><au>Mulichak, A.M.</au><au>Lewis, S.D.</au><au>Shafer, J.A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Crystal Structure of Human α-Thrombin Complexed with Hirugen and p-Amidinophenylpyruvate at 1.6 Å Resolution</atitle><jtitle>Archives of biochemistry and biophysics</jtitle><addtitle>Arch Biochem Biophys</addtitle><date>1995-09-10</date><risdate>1995</risdate><volume>322</volume><issue>1</issue><spage>198</spage><epage>203</epage><pages>198-203</pages><issn>0003-9861</issn><eissn>1096-0384</eissn><abstract>Crystals of human α-thrombin complexed with hirugen and the α-keto acid thrombin inhibitor APPA (
p-amidinophenylpyruvate) that diffract to 1.6 Å resolution were obtained by soaking an α-thrombin-hirugen crystal in a solution of APPA. The crystal structure was determined using the difference Fourier method and refined to an
R factor of 18.7% at 1.6 Å resolution. This structure is the highest resolution structure of the thrombin molecule that is currently available. With the exception of the region near Arg77A-Asn78, the structures of the thrombin and hirugen molecules in the ternary complex are similar to those reported for the thrombin-hirugen binary complex. As previously determined for the APPA-trypsin complex, the carbonyl carbon atom of APPA forms a covalent bond with Oγ of Ser195 of thrombin to yield a "transition-state" analog of the tetrahedral intermediate. Comparison of the specificity pocket of the APPA complexes of thrombin and trypsin reveals differences in hydrogen bonding and shows for the first time that the S1 site of thrombin is larger than that of trypsin and as a result thrombin may be able to accommodate a bulkier P1 group than trypsin.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>7574675</pmid><doi>10.1006/abbi.1995.1452</doi><tpages>6</tpages></addata></record> |
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| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | Amino Acid Sequence Binding Sites Crystallization Crystallography, X-Ray Hirudins - analogs & derivatives Hirudins - chemistry Hirudins - genetics Humans Hydrogen Bonding In Vitro Techniques Models, Molecular Molecular Sequence Data Molecular Structure Peptide Fragments - chemistry Peptide Fragments - genetics Phenylpyruvic Acids - chemistry Protein Conformation Thrombin - chemistry Thrombin - genetics Trypsin - chemistry |
| title | Crystal Structure of Human α-Thrombin Complexed with Hirugen and p-Amidinophenylpyruvate at 1.6 Å Resolution |
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