Escherichia coli cyclophilin B binds a highly distorted form of trans‐prolyl peptide isomer
Cyclophilins facilitate the peptidyl‐prolyl isomerization of a trans‐isomer to a cis‐isomer in the refolding process of unfolded proteins to recover the natural folding state with cis‐proline conformation. To date, only short peptides with a cis‐form proline have been observed in complexes of human...
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description | Cyclophilins facilitate the peptidyl‐prolyl isomerization of a trans‐isomer to a cis‐isomer in the refolding process of unfolded proteins to recover the natural folding state with cis‐proline conformation. To date, only short peptides with a cis‐form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans‐form proline, i.e. succinyl‐Ala‐trans‐Pro‐Ala‐p‐nitroanilide and acetyl‐Ala‐Ala‐trans‐Pro‐Ala‐amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis‐form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and Nη2 of Arg is formed to fix the peptide. On the other hand, in the cis‐isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans‐isomer formation of a hydrogen bond between CO preceding Ala‐Pro and His47 Nε2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala‐Pro. Although loss of double bond character of the amide bond of Ala‐Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character. |
doi_str_mv | 10.1111/j.1432-1033.2004.04321.x |
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To date, only short peptides with a cis‐form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans‐form proline, i.e. succinyl‐Ala‐trans‐Pro‐Ala‐p‐nitroanilide and acetyl‐Ala‐Ala‐trans‐Pro‐Ala‐amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis‐form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and Nη2 of Arg is formed to fix the peptide. On the other hand, in the cis‐isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans‐isomer formation of a hydrogen bond between CO preceding Ala‐Pro and His47 Nε2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala‐Pro. Although loss of double bond character of the amide bond of Ala‐Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character.</description><identifier>ISSN: 0014-2956</identifier><identifier>EISSN: 1432-1033</identifier><identifier>DOI: 10.1111/j.1432-1033.2004.04321.x</identifier><identifier>PMID: 15355356</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Science Ltd</publisher><subject>Amino Acid Sequence ; Amino Acid Substitution ; Crystallization ; cyclophilin ; Cyclophilins - genetics ; Cyclophilins - metabolism ; Escherichia coli ; Escherichia coli - metabolism ; Hydrogen Bonding ; Isomerism ; isozyme ; Models, Molecular ; Molecular Sequence Data ; peptide binding ; Peptides - chemistry ; Peptides - genetics ; Peptidylprolyl Isomerase ; peptidyl‐prolyl cis‐trans isomerase ; Proline - chemistry ; Proline - genetics ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; refolding ; Sequence Homology, Amino Acid ; Threonine - metabolism</subject><ispartof>European journal of biochemistry, 2004-09, Vol.271 (18), p.3794-3803</ispartof><rights>Copyright 2004 FEBS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3971-31771a8b3788887a3fde424b914f1c0dc2ac9b3aff524f15c9c2a424072dbe373</citedby><cites>FETCH-LOGICAL-c3971-31771a8b3788887a3fde424b914f1c0dc2ac9b3aff524f15c9c2a424072dbe373</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1432-1033.2004.04321.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1432-1033.2004.04321.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15355356$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Konno, Michiko</creatorcontrib><creatorcontrib>Sano, Yumi</creatorcontrib><creatorcontrib>Okudaira, Kayoko</creatorcontrib><creatorcontrib>Kawaguchi, Yoko</creatorcontrib><creatorcontrib>Yamagishi‐Ohmori, Yoko</creatorcontrib><creatorcontrib>Fushinobu, Shinya</creatorcontrib><creatorcontrib>Matsuzawa, Hiroshi</creatorcontrib><title>Escherichia coli cyclophilin B binds a highly distorted form of trans‐prolyl peptide isomer</title><title>European journal of biochemistry</title><addtitle>Eur J Biochem</addtitle><description>Cyclophilins facilitate the peptidyl‐prolyl isomerization of a trans‐isomer to a cis‐isomer in the refolding process of unfolded proteins to recover the natural folding state with cis‐proline conformation. To date, only short peptides with a cis‐form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans‐form proline, i.e. succinyl‐Ala‐trans‐Pro‐Ala‐p‐nitroanilide and acetyl‐Ala‐Ala‐trans‐Pro‐Ala‐amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis‐form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and Nη2 of Arg is formed to fix the peptide. On the other hand, in the cis‐isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans‐isomer formation of a hydrogen bond between CO preceding Ala‐Pro and His47 Nε2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala‐Pro. Although loss of double bond character of the amide bond of Ala‐Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character.</description><subject>Amino Acid Sequence</subject><subject>Amino Acid Substitution</subject><subject>Crystallization</subject><subject>cyclophilin</subject><subject>Cyclophilins - genetics</subject><subject>Cyclophilins - metabolism</subject><subject>Escherichia coli</subject><subject>Escherichia coli - metabolism</subject><subject>Hydrogen Bonding</subject><subject>Isomerism</subject><subject>isozyme</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>peptide binding</subject><subject>Peptides - chemistry</subject><subject>Peptides - genetics</subject><subject>Peptidylprolyl Isomerase</subject><subject>peptidyl‐prolyl cis‐trans isomerase</subject><subject>Proline - chemistry</subject><subject>Proline - genetics</subject><subject>Protein Conformation</subject><subject>Protein Folding</subject><subject>Protein Structure, Secondary</subject><subject>refolding</subject><subject>Sequence Homology, Amino Acid</subject><subject>Threonine - metabolism</subject><issn>0014-2956</issn><issn>1432-1033</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkdFOwyAUhonRuDl9BcOVd61Q2tLemLhlU5MlXqiXhlBKLQsdFbq43vkIPqNPInWLXuoJCYfDdw7k_wGAGIXYx-UqxDGJAowICSOE4hD5Iw63B2D8c3EIxgjhOIjyJB2BE-dWCKE0T-kxGOGEJH6lY_A8d6KWVolacSiMVlD0Qpu2Vlqt4RQWal06yGGtXmrdw1K5zthOlrAytoGmgp3la_f5_tFao3sNW9l2qpRQOdNIewqOKq6dPNvvE_C0mD_OboPl_c3d7HoZCJJTHBBMKeZZQWjmg3JSlTKO4iLHcYUFKkXERV4QXlVJ5CuJyH3FA4hGZSEJJRNwsZvrf_G6ka5jjXJCas3X0mwcS9Ms9Xj2J4hpFqE8Ix7MdqCwxjkrK9Za1XDbM4zY4AFbsUFqNkjNBg_Ytwds61vP929sikaWv4170T1wtQPelJb9vwezxXz6MKTkCx7_lnI</recordid><startdate>200409</startdate><enddate>200409</enddate><creator>Konno, Michiko</creator><creator>Sano, Yumi</creator><creator>Okudaira, Kayoko</creator><creator>Kawaguchi, Yoko</creator><creator>Yamagishi‐Ohmori, Yoko</creator><creator>Fushinobu, Shinya</creator><creator>Matsuzawa, Hiroshi</creator><general>Blackwell Science Ltd</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>7QL</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>200409</creationdate><title>Escherichia coli cyclophilin B binds a highly distorted form of trans‐prolyl peptide isomer</title><author>Konno, Michiko ; Sano, Yumi ; Okudaira, Kayoko ; Kawaguchi, Yoko ; Yamagishi‐Ohmori, Yoko ; Fushinobu, Shinya ; Matsuzawa, Hiroshi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3971-31771a8b3788887a3fde424b914f1c0dc2ac9b3aff524f15c9c2a424072dbe373</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Amino Acid Sequence</topic><topic>Amino Acid Substitution</topic><topic>Crystallization</topic><topic>cyclophilin</topic><topic>Cyclophilins - genetics</topic><topic>Cyclophilins - metabolism</topic><topic>Escherichia coli</topic><topic>Escherichia coli - metabolism</topic><topic>Hydrogen Bonding</topic><topic>Isomerism</topic><topic>isozyme</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>peptide binding</topic><topic>Peptides - chemistry</topic><topic>Peptides - genetics</topic><topic>Peptidylprolyl Isomerase</topic><topic>peptidyl‐prolyl cis‐trans isomerase</topic><topic>Proline - chemistry</topic><topic>Proline - genetics</topic><topic>Protein Conformation</topic><topic>Protein Folding</topic><topic>Protein Structure, Secondary</topic><topic>refolding</topic><topic>Sequence Homology, Amino Acid</topic><topic>Threonine - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Konno, Michiko</creatorcontrib><creatorcontrib>Sano, Yumi</creatorcontrib><creatorcontrib>Okudaira, Kayoko</creatorcontrib><creatorcontrib>Kawaguchi, Yoko</creatorcontrib><creatorcontrib>Yamagishi‐Ohmori, Yoko</creatorcontrib><creatorcontrib>Fushinobu, Shinya</creatorcontrib><creatorcontrib>Matsuzawa, Hiroshi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>European journal of biochemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Konno, Michiko</au><au>Sano, Yumi</au><au>Okudaira, Kayoko</au><au>Kawaguchi, Yoko</au><au>Yamagishi‐Ohmori, Yoko</au><au>Fushinobu, Shinya</au><au>Matsuzawa, Hiroshi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Escherichia coli cyclophilin B binds a highly distorted form of trans‐prolyl peptide isomer</atitle><jtitle>European journal of biochemistry</jtitle><addtitle>Eur J Biochem</addtitle><date>2004-09</date><risdate>2004</risdate><volume>271</volume><issue>18</issue><spage>3794</spage><epage>3803</epage><pages>3794-3803</pages><issn>0014-2956</issn><eissn>1432-1033</eissn><abstract>Cyclophilins facilitate the peptidyl‐prolyl isomerization of a trans‐isomer to a cis‐isomer in the refolding process of unfolded proteins to recover the natural folding state with cis‐proline conformation. To date, only short peptides with a cis‐form proline have been observed in complexes of human and Escherichia coli proteins of cyclophilin A, which is present in cytoplasm. The crystal structures analyzed in this study show two complexes in which peptides having a trans‐form proline, i.e. succinyl‐Ala‐trans‐Pro‐Ala‐p‐nitroanilide and acetyl‐Ala‐Ala‐trans‐Pro‐Ala‐amidomethylcoumarin, are bound on a K163T mutant of Escherichia coli cyclophilin B, the preprotein of which has a signal sequence. Comparison with cis‐form peptides bound to cyclophilin A reveals that in any case the proline ring is inserted into the hydrophobic pocket and a hydrogen bond between CO of Pro and Nη2 of Arg is formed to fix the peptide. On the other hand, in the cis‐isomer, the formation of two hydrogen bonds of NH and CO of Ala preceding Pro with the protein fixes the peptide, whereas in the trans‐isomer formation of a hydrogen bond between CO preceding Ala‐Pro and His47 Nε2 via a mediating water molecule allows the large distortion in the orientation of Ala of Ala‐Pro. Although loss of double bond character of the amide bond of Ala‐Pro is essential to the isomerization pathway occurring by rotating around its bond, these peptides have forms impossible to undergo proton transfer from the guanidyl group of Arg to the prolyl N atom, which induces loss of double bond character.</abstract><cop>Oxford, UK</cop><pub>Blackwell Science Ltd</pub><pmid>15355356</pmid><doi>10.1111/j.1432-1033.2004.04321.x</doi><tpages>10</tpages></addata></record> |
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subjects | Amino Acid Sequence Amino Acid Substitution Crystallization cyclophilin Cyclophilins - genetics Cyclophilins - metabolism Escherichia coli Escherichia coli - metabolism Hydrogen Bonding Isomerism isozyme Models, Molecular Molecular Sequence Data peptide binding Peptides - chemistry Peptides - genetics Peptidylprolyl Isomerase peptidyl‐prolyl cis‐trans isomerase Proline - chemistry Proline - genetics Protein Conformation Protein Folding Protein Structure, Secondary refolding Sequence Homology, Amino Acid Threonine - metabolism |
title | Escherichia coli cyclophilin B binds a highly distorted form of trans‐prolyl peptide isomer |
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