Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM
Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyan...
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| description | Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein. |
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A09DM</title><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Public Library of Science (PLoS) Journals Open Access</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Sonani, Ravi Raghav ; Gupta, Gagan Deep ; Madamwar, Datta ; Kumar, Vinay</creator><contributor>Wlodawer, Alexander</contributor><creatorcontrib>Sonani, Ravi Raghav ; Gupta, Gagan Deep ; Madamwar, Datta ; Kumar, Vinay ; Wlodawer, Alexander</creatorcontrib><description>Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0124580</identifier><identifier>PMID: 25923120</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algae ; Alternative energy sources ; Amino Acid Sequence ; Amino acids ; Bioinformatics ; Chlorophyll ; Chromophores ; Crystal lattices ; Crystal structure ; Crystallography ; Crystallography, X-Ray ; Cyanobacteria ; Cyanobacteria - metabolism ; Dimerization ; Energy absorption ; Fresh water ; Freshwater environments ; Hydrophobicity ; Light ; Models, Molecular ; Molecular Sequence Data ; Monomers ; Patel, Sardar ; PCB ; Phormidium ; Photosynthesis ; Photosynthetic apparatus ; Phycobilisomes - metabolism ; Phycocyanin ; Phycocyanin - chemistry ; Phycocyanin - isolation & purification ; Phycocyanin - metabolism ; Phycocyanobilin ; Polychlorinated biphenyls ; Protein folding ; Protein Structure, Tertiary ; Protein Subunits - chemistry ; Protein Subunits - isolation & purification ; Protein Subunits - metabolism ; Proteins ; Residues ; Rhodophyta ; Sequence Alignment ; Solar energy ; Solid state physics ; Stereochemistry ; Structure-function relationships ; Trimers ; X-ray crystallography</subject><ispartof>PloS one, 2015-04, Vol.10 (4), p.e0124580-e0124580</ispartof><rights>2015 Sonani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2015 Sonani et al 2015 Sonani et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-92476ca36013cd9cf4c407dd7d139b230219bf12fdfd94c3ddf3c27ef8be4d353</citedby><cites>FETCH-LOGICAL-c526t-92476ca36013cd9cf4c407dd7d139b230219bf12fdfd94c3ddf3c27ef8be4d353</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414346/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414346/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2095,2914,23846,27903,27904,53770,53772,79347,79348</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25923120$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Wlodawer, Alexander</contributor><creatorcontrib>Sonani, Ravi Raghav</creatorcontrib><creatorcontrib>Gupta, Gagan Deep</creatorcontrib><creatorcontrib>Madamwar, Datta</creatorcontrib><creatorcontrib>Kumar, Vinay</creatorcontrib><title>Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.</description><subject>Algae</subject><subject>Alternative energy sources</subject><subject>Amino Acid Sequence</subject><subject>Amino acids</subject><subject>Bioinformatics</subject><subject>Chlorophyll</subject><subject>Chromophores</subject><subject>Crystal lattices</subject><subject>Crystal structure</subject><subject>Crystallography</subject><subject>Crystallography, X-Ray</subject><subject>Cyanobacteria</subject><subject>Cyanobacteria - metabolism</subject><subject>Dimerization</subject><subject>Energy absorption</subject><subject>Fresh water</subject><subject>Freshwater environments</subject><subject>Hydrophobicity</subject><subject>Light</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Data</subject><subject>Monomers</subject><subject>Patel, Sardar</subject><subject>PCB</subject><subject>Phormidium</subject><subject>Photosynthesis</subject><subject>Photosynthetic apparatus</subject><subject>Phycobilisomes - metabolism</subject><subject>Phycocyanin</subject><subject>Phycocyanin - chemistry</subject><subject>Phycocyanin - isolation & purification</subject><subject>Phycocyanin - metabolism</subject><subject>Phycocyanobilin</subject><subject>Polychlorinated biphenyls</subject><subject>Protein folding</subject><subject>Protein Structure, Tertiary</subject><subject>Protein Subunits - chemistry</subject><subject>Protein Subunits - isolation & purification</subject><subject>Protein Subunits - metabolism</subject><subject>Proteins</subject><subject>Residues</subject><subject>Rhodophyta</subject><subject>Sequence Alignment</subject><subject>Solar energy</subject><subject>Solid state physics</subject><subject>Stereochemistry</subject><subject>Structure-function relationships</subject><subject>Trimers</subject><subject>X-ray crystallography</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptkttrFDEUxoMo9qL_geiAL33ZNbfJ5UVY1t6gRcH6HDK5dLNkJmMyI-x_72x3WlrxKYeT7_vlnPAB8AHBJSIcfdmmMXc6LvvUuSVEmNYCvgLHSBK8YBiS18_qI3BSyhbCmgjG3oIjXEtMEIbH4G6dd2XQsfo55NEMY3ZV8tUqxtRvdiaZne5CV_mc2upW59C5aj21UqPN4HIY2-rHJuU22H1Z-mW1gvLb7TvwxutY3Pv5PAW_Ls7v1leLm--X1-vVzcLUmA0LiSlnRhMGETFWGk8NhdxabhGRDSYQI9l4hL31VlJDrPXEYO68aBy1pCan4NOB28dU1PwhRSHGGcMTg0-K64PCJr1VfQ6tzjuVdFAPjZTvlc5DMNEpihgWHELrMKWwpoIZ2NRYeMg50kZOrK_za2PTOmtcN2QdX0Bf3nRho-7TH0UpooSyCXA2A3L6PboyqDYU42LUnUvjw9xcCIEpmaSf_5H-fzt6UJmcSsnOPw2DoNqH5NGl9iFRc0gm28fnizyZHlNB_gLgi7oI</recordid><startdate>20150429</startdate><enddate>20150429</enddate><creator>Sonani, Ravi Raghav</creator><creator>Gupta, Gagan Deep</creator><creator>Madamwar, Datta</creator><creator>Kumar, Vinay</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150429</creationdate><title>Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM</title><author>Sonani, Ravi Raghav ; Gupta, Gagan Deep ; Madamwar, Datta ; Kumar, Vinay</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-92476ca36013cd9cf4c407dd7d139b230219bf12fdfd94c3ddf3c27ef8be4d353</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Algae</topic><topic>Alternative energy sources</topic><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Bioinformatics</topic><topic>Chlorophyll</topic><topic>Chromophores</topic><topic>Crystal lattices</topic><topic>Crystal structure</topic><topic>Crystallography</topic><topic>Crystallography, X-Ray</topic><topic>Cyanobacteria</topic><topic>Cyanobacteria - metabolism</topic><topic>Dimerization</topic><topic>Energy absorption</topic><topic>Fresh water</topic><topic>Freshwater environments</topic><topic>Hydrophobicity</topic><topic>Light</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Data</topic><topic>Monomers</topic><topic>Patel, Sardar</topic><topic>PCB</topic><topic>Phormidium</topic><topic>Photosynthesis</topic><topic>Photosynthetic apparatus</topic><topic>Phycobilisomes - metabolism</topic><topic>Phycocyanin</topic><topic>Phycocyanin - chemistry</topic><topic>Phycocyanin - isolation & purification</topic><topic>Phycocyanin - metabolism</topic><topic>Phycocyanobilin</topic><topic>Polychlorinated biphenyls</topic><topic>Protein folding</topic><topic>Protein Structure, Tertiary</topic><topic>Protein Subunits - chemistry</topic><topic>Protein Subunits - isolation & purification</topic><topic>Protein Subunits - metabolism</topic><topic>Proteins</topic><topic>Residues</topic><topic>Rhodophyta</topic><topic>Sequence Alignment</topic><topic>Solar energy</topic><topic>Solid state physics</topic><topic>Stereochemistry</topic><topic>Structure-function relationships</topic><topic>Trimers</topic><topic>X-ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Sonani, Ravi Raghav</creatorcontrib><creatorcontrib>Gupta, Gagan Deep</creatorcontrib><creatorcontrib>Madamwar, Datta</creatorcontrib><creatorcontrib>Kumar, Vinay</creatorcontrib><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>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</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 Technology 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>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</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>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Sonani, Ravi Raghav</au><au>Gupta, Gagan Deep</au><au>Madamwar, Datta</au><au>Kumar, Vinay</au><au>Wlodawer, Alexander</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-04-29</date><risdate>2015</risdate><volume>10</volume><issue>4</issue><spage>e0124580</spage><epage>e0124580</epage><pages>e0124580-e0124580</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Isolated phycobilisome (PBS) sub-assemblies have been widely subjected to X-ray crystallography analysis to obtain greater insights into the structure-function relationship of this light harvesting complex. Allophycocyanin (APC) is the phycobiliprotein always found in the PBS core complex. Phycocyanobilin (PCB) chromophores, covalently bound to conserved Cys residues of α- and β- subunits of APC, are responsible for solar energy absorption from phycocyanin and for transfer to photosynthetic apparatus. In the known APC structures, heterodimers of α- and β- subunits (known as αβ monomers) assemble as trimer or hexamer. We here for the first time report the crystal structure of APC isolated from a marine cyanobacterium (Phormidium sp. A09DM). The crystal structure has been refined against all the observed data to the resolution of 2.51 Å to Rwork (Rfree) of 0.158 (0.229) with good stereochemistry of the atomic model. The Phormidium protein exists as a trimer of αβ monomers in solution and in crystal lattice. The overall tertiary structures of α- and β- subunits, and trimeric quaternary fold of the Phormidium protein resemble the other known APC structures. Also, configuration and conformation of the two covalently bound PCB chromophores in the marine APC are same as those observed in fresh water cyanobacteria and marine red algae. More hydrophobic residues, however, constitute the environment of the chromophore bound to α-subunit of the Phormidium protein, owing mainly to amino acid substitutions in the marine protein.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25923120</pmid><doi>10.1371/journal.pone.0124580</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Algae Alternative energy sources Amino Acid Sequence Amino acids Bioinformatics Chlorophyll Chromophores Crystal lattices Crystal structure Crystallography Crystallography, X-Ray Cyanobacteria Cyanobacteria - metabolism Dimerization Energy absorption Fresh water Freshwater environments Hydrophobicity Light Models, Molecular Molecular Sequence Data Monomers Patel, Sardar PCB Phormidium Photosynthesis Photosynthetic apparatus Phycobilisomes - metabolism Phycocyanin Phycocyanin - chemistry Phycocyanin - isolation & purification Phycocyanin - metabolism Phycocyanobilin Polychlorinated biphenyls Protein folding Protein Structure, Tertiary Protein Subunits - chemistry Protein Subunits - isolation & purification Protein Subunits - metabolism Proteins Residues Rhodophyta Sequence Alignment Solar energy Solid state physics Stereochemistry Structure-function relationships Trimers X-ray crystallography |
| title | Crystal Structure of Allophycocyanin from Marine Cyanobacterium Phormidium sp. A09DM |
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