Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA
The β-barrel assembly machinery (BAM) complex mediates the assembly of β-barrel membrane proteins in the outer membrane. BepA, formerly known as YfgC, interacts with the BAM complex and functions as a protease/chaperone for the enhancement of the assembly and/or degradation of β-barrel membrane prot...
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| Veröffentlicht in: | Journal of molecular biology 2019-02, Vol.431 (3), p.625-635 |
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| creator | Shahrizal, Mohammad Daimon, Yasushi Tanaka, Yoshiki Hayashi, Yugo Nakayama, Shintaro Iwaki, Shigehiro Narita, Shin-ichiro Kamikubo, Hironari Akiyama, Yoshinori Tsukazaki, Tomoya |
| description | The β-barrel assembly machinery (BAM) complex mediates the assembly of β-barrel membrane proteins in the outer membrane. BepA, formerly known as YfgC, interacts with the BAM complex and functions as a protease/chaperone for the enhancement of the assembly and/or degradation of β-barrel membrane proteins. To elucidate the molecular mechanism underlying the dual functions of BepA, its full-length three-dimensional structure is needed. Here, we report the crystal structure of full-length BepA at 2.6-Å resolution. BepA possesses an N-terminal protease domain and a C-terminal tetratricopeptide repeat domain, which interact with each other. Domain cross-linking by structure-guided introduction of disulfide bonds did not affect the activities of BepA in vivo, suggesting that the function of this protein does not involve domain rearrangement. The full-length BepA structure is compatible with the previously proposed docking model of BAM complex and tetratricopeptide repeat domain of BepA.
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•Crystal structure (2.6 Å) of full-length BepA, β-barrel assembly-enhancing protease BepA•Crystal structure represents both its functional and resting states.•Functional model of BepA was proposed. |
| doi_str_mv | 10.1016/j.jmb.2018.11.024 |
| format | Article |
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[Display omitted]
•Crystal structure (2.6 Å) of full-length BepA, β-barrel assembly-enhancing protease BepA•Crystal structure represents both its functional and resting states.•Functional model of BepA was proposed.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2018.11.024</identifier><identifier>PMID: 30521812</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Bacterial Outer Membrane Proteins - chemistry ; chaperon ; crystal structure ; Crystallography, X-Ray - methods ; Escherichia coli - chemistry ; Escherichia coli Proteins - chemistry ; Metalloproteases - chemistry ; Models, Molecular ; outer membrane ; protease ; protein biogenesis ; Protein Domains ; Protein Folding</subject><ispartof>Journal of molecular biology, 2019-02, Vol.431 (3), p.625-635</ispartof><rights>2018 Elsevier Ltd</rights><rights>Copyright © 2018 Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c463t-8056303beac187b0fac9689cc2ca7bcc2466d83de5e0a6820724ca6e41c8cc613</citedby><cites>FETCH-LOGICAL-c463t-8056303beac187b0fac9689cc2ca7bcc2466d83de5e0a6820724ca6e41c8cc613</cites><orcidid>0000-0003-4483-5408 ; 0000-0002-6157-0678</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0022283618310088$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30521812$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Shahrizal, Mohammad</creatorcontrib><creatorcontrib>Daimon, Yasushi</creatorcontrib><creatorcontrib>Tanaka, Yoshiki</creatorcontrib><creatorcontrib>Hayashi, Yugo</creatorcontrib><creatorcontrib>Nakayama, Shintaro</creatorcontrib><creatorcontrib>Iwaki, Shigehiro</creatorcontrib><creatorcontrib>Narita, Shin-ichiro</creatorcontrib><creatorcontrib>Kamikubo, Hironari</creatorcontrib><creatorcontrib>Akiyama, Yoshinori</creatorcontrib><creatorcontrib>Tsukazaki, Tomoya</creatorcontrib><title>Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>The β-barrel assembly machinery (BAM) complex mediates the assembly of β-barrel membrane proteins in the outer membrane. BepA, formerly known as YfgC, interacts with the BAM complex and functions as a protease/chaperone for the enhancement of the assembly and/or degradation of β-barrel membrane proteins. To elucidate the molecular mechanism underlying the dual functions of BepA, its full-length three-dimensional structure is needed. Here, we report the crystal structure of full-length BepA at 2.6-Å resolution. BepA possesses an N-terminal protease domain and a C-terminal tetratricopeptide repeat domain, which interact with each other. Domain cross-linking by structure-guided introduction of disulfide bonds did not affect the activities of BepA in vivo, suggesting that the function of this protein does not involve domain rearrangement. The full-length BepA structure is compatible with the previously proposed docking model of BAM complex and tetratricopeptide repeat domain of BepA.
[Display omitted]
•Crystal structure (2.6 Å) of full-length BepA, β-barrel assembly-enhancing protease BepA•Crystal structure represents both its functional and resting states.•Functional model of BepA was proposed.</description><subject>Bacterial Outer Membrane Proteins - chemistry</subject><subject>chaperon</subject><subject>crystal structure</subject><subject>Crystallography, X-Ray - methods</subject><subject>Escherichia coli - chemistry</subject><subject>Escherichia coli Proteins - chemistry</subject><subject>Metalloproteases - chemistry</subject><subject>Models, Molecular</subject><subject>outer membrane</subject><subject>protease</subject><subject>protein biogenesis</subject><subject>Protein Domains</subject><subject>Protein Folding</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE1O3EAQhVsoCAbCAbKJvMzGTlW33e5RVjOjgURCAgmybrXL5dAj_0y6bSSulYNwphiGZMnqqaTvPak-IT4hZAiov-6yXVdlEtBkiBnI_EgsEMwyNVqZD2IBIGUqjdKn4izGHQAUKjcn4lRBIdGgXIi7uzFMNE7BtcnaRR-TZgjJ-MDJ5dTT6Ic-GZrX-_lPunYhcJusYuSuap_Sbf_gevL9r-Q2DCO7yMma96uP4rhxbeSLtzwXPy-395vv6fXN1Y_N6jqlXKsxNVBoBapiR2jKChpHS22WRJJcWc2Ra10bVXPB4LSRUMqcnOYcyRBpVOfiy2F3H4bfE8fRdj4St63reZiilViUWs-bekbxgFIYYgzc2H3wnQtPFsG-uLQ7O7u0Ly4top1dzp3Pb_NT1XH9v_FP3gx8OwA8P_noOdhInnvi2gem0daDf2f-L4bChJU</recordid><startdate>20190201</startdate><enddate>20190201</enddate><creator>Shahrizal, Mohammad</creator><creator>Daimon, Yasushi</creator><creator>Tanaka, Yoshiki</creator><creator>Hayashi, Yugo</creator><creator>Nakayama, Shintaro</creator><creator>Iwaki, Shigehiro</creator><creator>Narita, Shin-ichiro</creator><creator>Kamikubo, Hironari</creator><creator>Akiyama, Yoshinori</creator><creator>Tsukazaki, Tomoya</creator><general>Elsevier 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>7X8</scope><orcidid>https://orcid.org/0000-0003-4483-5408</orcidid><orcidid>https://orcid.org/0000-0002-6157-0678</orcidid></search><sort><creationdate>20190201</creationdate><title>Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA</title><author>Shahrizal, Mohammad ; Daimon, Yasushi ; Tanaka, Yoshiki ; Hayashi, Yugo ; Nakayama, Shintaro ; Iwaki, Shigehiro ; Narita, Shin-ichiro ; Kamikubo, Hironari ; Akiyama, Yoshinori ; Tsukazaki, Tomoya</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c463t-8056303beac187b0fac9689cc2ca7bcc2466d83de5e0a6820724ca6e41c8cc613</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Bacterial Outer Membrane Proteins - chemistry</topic><topic>chaperon</topic><topic>crystal structure</topic><topic>Crystallography, X-Ray - methods</topic><topic>Escherichia coli - chemistry</topic><topic>Escherichia coli Proteins - chemistry</topic><topic>Metalloproteases - chemistry</topic><topic>Models, Molecular</topic><topic>outer membrane</topic><topic>protease</topic><topic>protein biogenesis</topic><topic>Protein Domains</topic><topic>Protein Folding</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Shahrizal, Mohammad</creatorcontrib><creatorcontrib>Daimon, Yasushi</creatorcontrib><creatorcontrib>Tanaka, Yoshiki</creatorcontrib><creatorcontrib>Hayashi, Yugo</creatorcontrib><creatorcontrib>Nakayama, Shintaro</creatorcontrib><creatorcontrib>Iwaki, Shigehiro</creatorcontrib><creatorcontrib>Narita, Shin-ichiro</creatorcontrib><creatorcontrib>Kamikubo, Hironari</creatorcontrib><creatorcontrib>Akiyama, Yoshinori</creatorcontrib><creatorcontrib>Tsukazaki, Tomoya</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>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shahrizal, Mohammad</au><au>Daimon, Yasushi</au><au>Tanaka, Yoshiki</au><au>Hayashi, Yugo</au><au>Nakayama, Shintaro</au><au>Iwaki, Shigehiro</au><au>Narita, Shin-ichiro</au><au>Kamikubo, Hironari</au><au>Akiyama, Yoshinori</au><au>Tsukazaki, Tomoya</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2019-02-01</date><risdate>2019</risdate><volume>431</volume><issue>3</issue><spage>625</spage><epage>635</epage><pages>625-635</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>The β-barrel assembly machinery (BAM) complex mediates the assembly of β-barrel membrane proteins in the outer membrane. BepA, formerly known as YfgC, interacts with the BAM complex and functions as a protease/chaperone for the enhancement of the assembly and/or degradation of β-barrel membrane proteins. To elucidate the molecular mechanism underlying the dual functions of BepA, its full-length three-dimensional structure is needed. Here, we report the crystal structure of full-length BepA at 2.6-Å resolution. BepA possesses an N-terminal protease domain and a C-terminal tetratricopeptide repeat domain, which interact with each other. Domain cross-linking by structure-guided introduction of disulfide bonds did not affect the activities of BepA in vivo, suggesting that the function of this protein does not involve domain rearrangement. The full-length BepA structure is compatible with the previously proposed docking model of BAM complex and tetratricopeptide repeat domain of BepA.
[Display omitted]
•Crystal structure (2.6 Å) of full-length BepA, β-barrel assembly-enhancing protease BepA•Crystal structure represents both its functional and resting states.•Functional model of BepA was proposed.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>30521812</pmid><doi>10.1016/j.jmb.2018.11.024</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0003-4483-5408</orcidid><orcidid>https://orcid.org/0000-0002-6157-0678</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Bacterial Outer Membrane Proteins - chemistry chaperon crystal structure Crystallography, X-Ray - methods Escherichia coli - chemistry Escherichia coli Proteins - chemistry Metalloproteases - chemistry Models, Molecular outer membrane protease protein biogenesis Protein Domains Protein Folding |
| title | Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA |
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