Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds
Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evo...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2008-02, Vol.105 (7), p.2343-2348 |
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| container_title | Proceedings of the National Academy of Sciences - PNAS |
| container_volume | 105 |
| creator | Roessler, Christian G Hall, Branwen M Anderson, William J Ingram, Wendy M Roberts, Sue A Montfort, William R Cordes, Matthew H.J |
| description | Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and λ. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and λ. The domains show 40% sequence identity but differ by switching of α-helix to β-sheet in a C-terminal region spanning [almost equal to]25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization. |
| doi_str_mv | 10.1073/pnas.0711589105 |
| format | Article |
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For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and λ. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and λ. The domains show 40% sequence identity but differ by switching of α-helix to β-sheet in a C-terminal region spanning [almost equal to]25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0711589105</identifier><identifier>PMID: 18227506</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Amino Acid Sequence ; Amino acids ; Bacteriophages ; Biochemistry ; Biological Sciences ; Circular Dichroism ; Crystal structure ; Crystallography, X-Ray ; Dimerization ; Dimers ; Divergent evolution ; DNA ; DNA-Binding Proteins - chemistry ; Evolution ; Models, Molecular ; Molecular Sequence Data ; Phage P22 ; Protein folding ; Protein Structure, Tertiary ; Proteins ; Regional identity ; Repressor Proteins - chemistry ; Sodium ; Viral Regulatory and Accessory Proteins - chemistry</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2008-02, Vol.105 (7), p.2343-2348</ispartof><rights>Copyright 2008 The National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Feb 19, 2008</rights><rights>2008 by The National Academy of Sciences of the USA</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c550t-90fa971429e80cae4e0a96358a163d6b03d15e5877fae3a2dfe01cfa512e53433</citedby><cites>FETCH-LOGICAL-c550t-90fa971429e80cae4e0a96358a163d6b03d15e5877fae3a2dfe01cfa512e53433</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/105/7.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/25451468$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/25451468$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,803,885,27923,27924,53790,53792,58016,58249</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18227506$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Roessler, Christian G</creatorcontrib><creatorcontrib>Hall, Branwen M</creatorcontrib><creatorcontrib>Anderson, William J</creatorcontrib><creatorcontrib>Ingram, Wendy M</creatorcontrib><creatorcontrib>Roberts, Sue A</creatorcontrib><creatorcontrib>Montfort, William R</creatorcontrib><creatorcontrib>Cordes, Matthew H.J</creatorcontrib><title>Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Proteins that share common ancestry may differ in structure and function because of divergent evolution of their amino acid sequences. For a typical diverse protein superfamily, the properties of a few scattered members are known from experiment. A satisfying picture of functional and structural evolution in relation to sequence changes, however, may require characterization of a larger, well chosen subset. Here, we employ a "stepping-stone" method, based on transitive homology, to target sequences intermediate between two related proteins with known divergent properties. We apply the approach to the question of how new protein folds can evolve from preexisting folds and, in particular, to an evolutionary change in secondary structure and oligomeric state in the Cro family of bacteriophage transcription factors, initially identified by sequence-structure comparison of distant homologs from phages P22 and λ. We report crystal structures of two Cro proteins, Xfaso 1 and Pfl 6, with sequences intermediate between those of P22 and λ. The domains show 40% sequence identity but differ by switching of α-helix to β-sheet in a C-terminal region spanning [almost equal to]25 residues. 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The domains show 40% sequence identity but differ by switching of α-helix to β-sheet in a C-terminal region spanning [almost equal to]25 residues. Sedimentation analysis also suggests a correlation between helix-to-sheet conversion and strengthened dimerization.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>18227506</pmid><doi>10.1073/pnas.0711589105</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence Amino acids Bacteriophages Biochemistry Biological Sciences Circular Dichroism Crystal structure Crystallography, X-Ray Dimerization Dimers Divergent evolution DNA DNA-Binding Proteins - chemistry Evolution Models, Molecular Molecular Sequence Data Phage P22 Protein folding Protein Structure, Tertiary Proteins Regional identity Repressor Proteins - chemistry Sodium Viral Regulatory and Accessory Proteins - chemistry |
| title | Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds |
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