2bgj: Difference between revisions

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-[[Image:2bgj.png|left|200px]]
-<!--
+==X-Ray Structure of the Ferredoxin-NADP(H) Reductase from Rhodobacter capsulatus at 2.1 Angstroms==
-The line below this paragraph, containing "STRUCTURE_2bgj", creates the "Structure Box" on the page.
+<StructureSection load='2bgj' size='340' side='right'caption='[[2bgj]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2bgj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BGJ FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-{{STRUCTURE_2bgj|  PDB=2bgj  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bgj OCA], [https://pdbe.org/2bgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bgj RCSB], [https://www.ebi.ac.uk/pdbsum/2bgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bgj ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FENR_RHOCA FENR_RHOCA] Transports electrons between flavodoxin or ferredoxin and NADPH.<ref>PMID:14572660</ref> <ref>PMID:16128574</ref> <ref>PMID:24016470</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bg/2bgj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=2bgj ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The photosynthetic bacterium Rhodobacter capsulatus contains a ferredoxin (flavodoxin)-NADP(H) oxidoreductase (FPR) that catalyzes electron transfer between NADP(H) and ferredoxin or flavodoxin. The structure of the enzyme, determined by X-ray crystallography, contains two domains harboring the FAD and NADP(H) binding sites, as is typical of the FPR structural family. The FAD molecule is in a hairpin conformation in which stacking interactions can be established between the dimethylisoalloxazine and adenine moieties. The midpoint redox potentials of the various transitions undergone by R. capsulatus FPR were similar to those reported for their counterparts involved in oxygenic photosynthesis, but its catalytic activity is orders of magnitude lower (1-2 s(-)(1) versus 200-500 s(-)(1)) as is true for most of its prokaryotic homologues. To identify the mechanistic basis for the slow turnover in the bacterial enzymes, we dissected the R. capsulatus FPR reaction into hydride transfer and electron transfer steps, and determined their rates using stopped-flow methods. Hydride exchange between the enzyme and NADP(H) occurred at 30-150 s(-)(1), indicating that this half-reaction does not limit FPR activity. In contrast, electron transfer to flavodoxin proceeds at 2.7 s(-)(1), in the range of steady-state catalysis. Flavodoxin semiquinone was a better electron acceptor for FPR than oxidized flavodoxin under both single turnover and steady-state conditions. The results indicate that one-electron reduction of oxidized flavodoxin limits the enzyme activity in vitro, and support the notion that flavodoxin oscillates between the semiquinone and fully reduced states when FPR operates in vivo.
-===X-RAY STRUCTURE OF THE FERREDOXIN-NADP(H) REDUCTASE FROM RHODOBACTER CAPSULATUS AT 2.1 ANGSTROMS===
+The ferredoxin-NADP(H) reductase from Rhodobacter capsulatus: molecular structure and catalytic mechanism.,Nogues I, Perez-Dorado I, Frago S, Bittel C, Mayhew SG, Gomez-Moreno C, Hermoso JA, Medina M, Cortez N, Carrillo N Biochemistry. 2005 Sep 6;44(35):11730-40. PMID:16128574<ref>PMID:16128574</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16128574}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2bgj" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16128574 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16128574}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[2bgj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BGJ OCA].
-==Reference==
-<ref group="xtra">PMID:16128574</ref><ref group="xtra">PMID:15583382</ref><ref group="xtra">PMID:14572660</ref><references group="xtra"/>
-[[Category: Rhodobacter capsulatus]]
-[[Category: Bittel, C.]]
-[[Category: Carrillo, N.]]
-[[Category: Cortez, N.]]
-[[Category: Frago, S.]]
-[[Category: Gomez-Moreno, C.]]
-[[Category: Hermoso, J A.]]
-[[Category: Mayhew, S G.]]
-[[Category: Medina, M.]]
-[[Category: Nogues, I.]]
-[[Category: Perez-Dorado, J I.]]
-[[Category: Electron transfer]]
-[[Category: Flavoprotein]]
-[[Category: Oxidoreductase]]
 [[Category: Rhodobacter capsulatus]]
+[[Category: Bittel C]]
+[[Category: Carrillo N]]
+[[Category: Cortez N]]
+[[Category: Frago S]]
+[[Category: Gomez-Moreno C]]
+[[Category: Hermoso JA]]
+[[Category: Mayhew SG]]
+[[Category: Medina M]]
+[[Category: Nogues I]]
+[[Category: Perez-Dorado JI]]