2vcl

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{{Seed}}
 
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[[Image:2vcl.png|left|200px]]
 
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==Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in the substrate free form==
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The line below this paragraph, containing "STRUCTURE_2vcl", creates the "Structure Box" on the page.
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<StructureSection load='2vcl' size='340' side='right'caption='[[2vcl]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2vcl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpprm Bpprm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VCL FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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{{STRUCTURE_2vcl| PDB=2vcl | SCENE= }}
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2vck|2vck]], [[2vgr|2vgr]]</div></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phycoerythrobilin_synthase Phycoerythrobilin synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.7.6 1.3.7.6] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vcl OCA], [https://pdbe.org/2vcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vcl RCSB], [https://www.ebi.ac.uk/pdbsum/2vcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vcl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/PEBS_BPPRM PEBS_BPPRM]] Plays a role in phycoerythrobilin biosynthesis, the red pigment chromophore photosynthetically active biliproteins of the host cyanobacteria. Uses a four-electron reduction to carry out the reactions catalyzed by two enzymes (EC 1.3.7.2 and EC 1.3.7.3) in host.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vc/2vcl_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vcl ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The reddish purple open chain tetrapyrrole pigment phycoerythrobilin (PEB; A(lambdamax) approximately 550 nm) is an essential chromophore of the light-harvesting phycobiliproteins of most cyanobacteria, red algae, and cryptomonads. The enzyme phycoerythrobilin synthase (PebS), recently discovered in a marine virus infecting oceanic cyanobacteria of the genus Prochlorococcus (cyanophage PSSM-2), is a new member of the ferredoxin-dependent bilin reductase (FDBR) family. In a formal four-electron reduction, the substrate biliverdin IXalpha is reduced to yield 3Z-PEB, a reaction that commonly requires the action of two individual FDBRs. The first reaction catalyzed by PebS is the reduction of the 15,16-methine bridge of the biliverdin IXalpha tetrapyrrole system. This reaction is exclusive to PEB biosynthetic enzymes. The second reduction site is the A-ring 2,3,3(1),3(2)-diene system, the most common target of FDBRs. Here, we present the first crystal structures of a PEB biosynthetic enzyme. Structures of the substrate complex were solved at 1.8- and 2.1-A resolution and of the substrate-free form at 1.55-A resolution. The overall folding revealed an alpha/beta/alpha-sandwich with similarity to the structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA). The substrate-binding site is located between the central beta-sheet and C-terminal alpha-helices. Eight refined molecules with bound substrate, from two different crystal forms, revealed a high flexibility of the substrate-binding pocket. The substrate was found to be either in a planar porphyrin-like conformation or in a helical conformation and is coordinated by a conserved aspartate/asparagine pair from the beta-sheet side. From the alpha-helix side, a conserved highly flexible aspartate/proline pair is involved in substrate binding and presumably catalysis.
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===STRUCTURE OF PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN THE SUBSTRATE FREE FORM===
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Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form.,Dammeyer T, Hofmann E, Frankenberg-Dinkel N J Biol Chem. 2008 Oct 10;283(41):27547-54. Epub 2008 Jul 28. PMID:18662988<ref>PMID:18662988</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18662988}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2vcl" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18662988 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18662988}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Bpprm]]
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2VCL is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Viruses Viruses]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VCL OCA].
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[[Category: Large Structures]]
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[[Category: Phycoerythrobilin synthase]]
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==Reference==
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[[Category: Dammeyer, T]]
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Phycoerythrobilin synthase (PebS) of a marine virus crystal structures of the biliverdin-complex and the substrate free form., Dammeyer T, Hofmann E, Frankenberg-Dinkel N, J Biol Chem. 2008 Jul 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18662988 18662988]
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[[Category: Frankenberg-Dinkel, N]]
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[[Category: Oxidoreductase]]
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[[Category: Hofmann, E]]
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[[Category: Single protein]]
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[[Category: Viruses]]
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[[Category: Dammeyer, T.]]
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[[Category: Frankenberg-Dinkel, N.]]
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[[Category: Hofmann, E.]]
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[[Category: Biliverdin ixa]]
[[Category: Biliverdin ixa]]
[[Category: Biliverdin reductase]]
[[Category: Biliverdin reductase]]
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[[Category: Phycoerythrobilin]]
[[Category: Phycoerythrobilin]]
[[Category: Prochlorococcus]]
[[Category: Prochlorococcus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 15 20:20:42 2008''
 

Current revision

Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in the substrate free form

PDB ID 2vcl

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