A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation
The crystal structure of a collagen‐binding domain (CBD) with an N‐terminal domain linker from Clostridium histolyticum class I collagenase was determined at 1.00 Å resolution in the absence of calcium (1NQJ) and at 1.65 Å resolution in the presence of calcium (1NQD). The mature enzyme is composed o...
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| Veröffentlicht in: | EMBO Journal 2003-04, Vol.22 (8), p.1743-1752 |
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| creator | Wilson, Jeffrey J. Matsushita, Osamu Okabe, Akinobu Sakon, Joshua |
| description | The crystal structure of a collagen‐binding domain (CBD) with an N‐terminal domain linker from
Clostridium histolyticum
class I collagenase was determined at 1.00 Å resolution in the absence of calcium (1NQJ) and at 1.65 Å resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12‐residue‐long linker is found at the N‐terminus of each CBD. In the absence of calcium, the CBD reveals a β‐sheet sandwich fold with the linker adopting an α‐helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new β‐strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen‐binding studies allow us to identify the collagen‐binding surface of the protein and propose likely collagen–protein binding models. |
| doi_str_mv | 10.1093/emboj/cdg172 |
| format | Article |
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Clostridium histolyticum
class I collagenase was determined at 1.00 Å resolution in the absence of calcium (1NQJ) and at 1.65 Å resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12‐residue‐long linker is found at the N‐terminus of each CBD. In the absence of calcium, the CBD reveals a β‐sheet sandwich fold with the linker adopting an α‐helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new β‐strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen‐binding studies allow us to identify the collagen‐binding surface of the protein and propose likely collagen–protein binding models.</description><identifier>ISSN: 0261-4189</identifier><identifier>ISSN: 1460-2075</identifier><identifier>EISSN: 1460-2075</identifier><identifier>DOI: 10.1093/emboj/cdg172</identifier><identifier>PMID: 12682007</identifier><identifier>CODEN: EMJODG</identifier><language>eng</language><publisher>Chichester, UK: John Wiley & Sons, Ltd</publisher><subject>Amino Acid Sequence ; BACTERIA ; Bacterial Proteins - chemistry ; Bacterial Proteins - genetics ; Bacterial Proteins - metabolism ; BASIC BIOLOGICAL SCIENCES ; Binding Sites ; Calcium ; Calcium - metabolism ; CALCIUM COMPOUNDS ; calcium-induced conformational change ; COLLAGEN ; Collagen - genetics ; Collagen - metabolism ; Crystallography, X-Ray ; domain reorientation ; EMBO23 ; EMBO40 ; extracellular calcium-binding protein ; Light scattering ; Microbial Collagenase - chemistry ; Microbial Collagenase - genetics ; Microbial Collagenase - metabolism ; Models, Molecular ; Molecular Sequence Data ; molecular switch ; Mutagenesis, Site-Directed ; NATIONAL SYNCHROTRON LIGHT SOURCE ; ORIENTATION ; Peptides - genetics ; Peptides - metabolism ; Protein Binding ; Protein Denaturation ; Protein Structure, Tertiary ; Sequence Alignment ; square antiprismatic ; Urea - metabolism</subject><ispartof>EMBO Journal, 2003-04, Vol.22 (8), p.1743-1752</ispartof><rights>European Molecular Biology Organization 2003</rights><rights>Copyright © 2003 European Molecular Biology Organization</rights><rights>Copyright Oxford University Press(England) Apr 15, 2003</rights><rights>Copyright © 2003 European Molecular Biology Organization 2003</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c6091-36952bd354cce78ddd3b10afd7613812e9ed968dab581bf4509564a0ff50cf1f3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC154464/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC154464/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,1417,1433,27924,27925,45574,45575,46409,46833,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12682007$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/15008216$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Wilson, Jeffrey J.</creatorcontrib><creatorcontrib>Matsushita, Osamu</creatorcontrib><creatorcontrib>Okabe, Akinobu</creatorcontrib><creatorcontrib>Sakon, Joshua</creatorcontrib><creatorcontrib>Brookhaven National Laboratory, National Synchrotron Light Source (US)</creatorcontrib><title>A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation</title><title>EMBO Journal</title><addtitle>EMBO J</addtitle><addtitle>EMBO J</addtitle><description>The crystal structure of a collagen‐binding domain (CBD) with an N‐terminal domain linker from
Clostridium histolyticum
class I collagenase was determined at 1.00 Å resolution in the absence of calcium (1NQJ) and at 1.65 Å resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12‐residue‐long linker is found at the N‐terminus of each CBD. In the absence of calcium, the CBD reveals a β‐sheet sandwich fold with the linker adopting an α‐helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new β‐strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen‐binding studies allow us to identify the collagen‐binding surface of the protein and propose likely collagen–protein binding models.</description><subject>Amino Acid Sequence</subject><subject>BACTERIA</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Proteins - metabolism</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>Binding Sites</subject><subject>Calcium</subject><subject>Calcium - metabolism</subject><subject>CALCIUM COMPOUNDS</subject><subject>calcium-induced conformational change</subject><subject>COLLAGEN</subject><subject>Collagen - genetics</subject><subject>Collagen - metabolism</subject><subject>Crystallography, X-Ray</subject><subject>domain reorientation</subject><subject>EMBO23</subject><subject>EMBO40</subject><subject>extracellular calcium-binding protein</subject><subject>Light scattering</subject><subject>Microbial Collagenase - chemistry</subject><subject>Microbial Collagenase - genetics</subject><subject>Microbial Collagenase - metabolism</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>molecular switch</subject><subject>Mutagenesis, Site-Directed</subject><subject>NATIONAL SYNCHROTRON LIGHT SOURCE</subject><subject>ORIENTATION</subject><subject>Peptides - genetics</subject><subject>Peptides - metabolism</subject><subject>Protein Binding</subject><subject>Protein Denaturation</subject><subject>Protein Structure, Tertiary</subject><subject>Sequence Alignment</subject><subject>square antiprismatic</subject><subject>Urea - metabolism</subject><issn>0261-4189</issn><issn>1460-2075</issn><issn>1460-2075</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>8G5</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNp9kTtz1DAURj0MDNkEOloYD5mhwuTKth4uKEIICyRAAQylkCXZq40tBUlOyL9H4GUJj6FSoXPu68uyewieIGiqAz22bn0gVY9oeSNboJpAUQLFN7MFlAQVNWLNTrYbwhoAMKPodraDSsJKALrIPh_mrZBReyOGXLphEL22RWusMrbPlRuFsfmliavcugudEDFIM41bYnTRdEm00bsh_BScN9pGEY2zd7JbnRiCvrt597KPL44_HL0sTt8tXx0dnhaSQIOKijS4bFWFayk1ZUqpqkUgOkUJqhgqdaNVQ5gSLWao7WoMDSa1gK7DIDvUVXvZ07nu-dSOWsnU34uBn3szCn_FnTD89x9rVrx3FxzhuiZ18vdn34VoeJAmarlKe1ktY2IAWIlIoh5tunj3ZdIh8tEEqdPZrHZT4IjRqk5nTuDDP8C1m7xNF-AobZpyYE2CHs-Q9C4Er7vtuAj493D5j3D5HG7CH1xf8Re8STMBeAYuzaCv_luMH7959priBgNDyStmLyTF9tpfG_bfg9yfeSvi5PW20V_1TIj66_Zb-DNOaEUx__R2yckS3j-HE8ZPqm-I_dyg</recordid><startdate>20030415</startdate><enddate>20030415</enddate><creator>Wilson, Jeffrey J.</creator><creator>Matsushita, Osamu</creator><creator>Okabe, Akinobu</creator><creator>Sakon, Joshua</creator><general>John Wiley & Sons, Ltd</general><general>Nature Publishing Group UK</general><general>Blackwell Publishing Ltd</general><general>Oxford University Press</general><scope>BSCLL</scope><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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>M7N</scope><scope>M7P</scope><scope>MBDVC</scope><scope>P64</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>RC3</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20030415</creationdate><title>A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation</title><author>Wilson, Jeffrey J. ; Matsushita, Osamu ; Okabe, Akinobu ; Sakon, Joshua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c6091-36952bd354cce78ddd3b10afd7613812e9ed968dab581bf4509564a0ff50cf1f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Amino Acid Sequence</topic><topic>BACTERIA</topic><topic>Bacterial Proteins - chemistry</topic><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Proteins - metabolism</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>Binding Sites</topic><topic>Calcium</topic><topic>Calcium - metabolism</topic><topic>CALCIUM COMPOUNDS</topic><topic>calcium-induced conformational change</topic><topic>COLLAGEN</topic><topic>Collagen - genetics</topic><topic>Collagen - metabolism</topic><topic>Crystallography, X-Ray</topic><topic>domain reorientation</topic><topic>EMBO23</topic><topic>EMBO40</topic><topic>extracellular calcium-binding protein</topic><topic>Light scattering</topic><topic>Microbial Collagenase - chemistry</topic><topic>Microbial Collagenase - genetics</topic><topic>Microbial Collagenase - metabolism</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>molecular switch</topic><topic>Mutagenesis, Site-Directed</topic><topic>NATIONAL SYNCHROTRON LIGHT SOURCE</topic><topic>ORIENTATION</topic><topic>Peptides - genetics</topic><topic>Peptides - metabolism</topic><topic>Protein Binding</topic><topic>Protein Denaturation</topic><topic>Protein Structure, Tertiary</topic><topic>Sequence Alignment</topic><topic>square antiprismatic</topic><topic>Urea - metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wilson, Jeffrey J.</creatorcontrib><creatorcontrib>Matsushita, Osamu</creatorcontrib><creatorcontrib>Okabe, Akinobu</creatorcontrib><creatorcontrib>Sakon, Joshua</creatorcontrib><creatorcontrib>Brookhaven National Laboratory, National Synchrotron Light Source (US)</creatorcontrib><collection>Istex</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Research Library</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Research Library (Corporate)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>EMBO Journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wilson, Jeffrey J.</au><au>Matsushita, Osamu</au><au>Okabe, Akinobu</au><au>Sakon, Joshua</au><aucorp>Brookhaven National Laboratory, National Synchrotron Light Source (US)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation</atitle><jtitle>EMBO Journal</jtitle><stitle>EMBO J</stitle><addtitle>EMBO J</addtitle><date>2003-04-15</date><risdate>2003</risdate><volume>22</volume><issue>8</issue><spage>1743</spage><epage>1752</epage><pages>1743-1752</pages><issn>0261-4189</issn><issn>1460-2075</issn><eissn>1460-2075</eissn><coden>EMJODG</coden><abstract>The crystal structure of a collagen‐binding domain (CBD) with an N‐terminal domain linker from
Clostridium histolyticum
class I collagenase was determined at 1.00 Å resolution in the absence of calcium (1NQJ) and at 1.65 Å resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12‐residue‐long linker is found at the N‐terminus of each CBD. In the absence of calcium, the CBD reveals a β‐sheet sandwich fold with the linker adopting an α‐helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new β‐strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen‐binding studies allow us to identify the collagen‐binding surface of the protein and propose likely collagen–protein binding models.</abstract><cop>Chichester, UK</cop><pub>John Wiley & Sons, Ltd</pub><pmid>12682007</pmid><doi>10.1093/emboj/cdg172</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Amino Acid Sequence BACTERIA Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism BASIC BIOLOGICAL SCIENCES Binding Sites Calcium Calcium - metabolism CALCIUM COMPOUNDS calcium-induced conformational change COLLAGEN Collagen - genetics Collagen - metabolism Crystallography, X-Ray domain reorientation EMBO23 EMBO40 extracellular calcium-binding protein Light scattering Microbial Collagenase - chemistry Microbial Collagenase - genetics Microbial Collagenase - metabolism Models, Molecular Molecular Sequence Data molecular switch Mutagenesis, Site-Directed NATIONAL SYNCHROTRON LIGHT SOURCE ORIENTATION Peptides - genetics Peptides - metabolism Protein Binding Protein Denaturation Protein Structure, Tertiary Sequence Alignment square antiprismatic Urea - metabolism |
| title | A bacterial collagen-binding domain with novel calcium-binding motif controls domain orientation |
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