2e4p: Difference between revisions

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-{{Seed}}
-[[Image:2e4p.png|left|200px]]
-<!--
+==Crystal structure of BphA3 (oxidized form)==
-The line below this paragraph, containing "STRUCTURE_2e4p", creates the "Structure Box" on the page.
+<StructureSection load='2e4p' size='340' side='right'caption='[[2e4p]], [[Resolution|resolution]] 2.00&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'>[[2e4p]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E4P 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&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2e4p|  PDB=2e4p  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e4p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e4p OCA], [https://pdbe.org/2e4p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e4p RCSB], [https://www.ebi.ac.uk/pdbsum/2e4p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e4p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BPHA3_PSES1 BPHA3_PSES1] This protein seems to be a 2Fe-2S ferredoxin.
+== 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/e4/2e4p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2e4p ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The electron transfer system of the biphenyl dioxygenase BphA, which is derived from Acidovorax sp. (formally Pseudomonas sp.) strain KKS102, is composed of an FAD-containing NADH-ferredoxin reductase (BphA4) and a Rieske-type [2Fe-2S] ferredoxin (BphA3). Biochemical studies have suggested that the whole electron transfer process from NADH to BphA3 comprises three consecutive elementary electron-transfer reactions, in which BphA3 and BphA4 interact transiently in a redox-dependent manner. Initially, BphA4 receives two electrons from NADH. The reduced BphA4 then delivers one electron each to the [2Fe-2S] cluster of the two BphA3 molecules through redox-dependent transient interactions. The reduced BphA3 transports the electron to BphA1A2, a terminal oxygenase, to support the activation of dioxygen for biphenyl dihydroxylation. In order to elucidate the molecular mechanisms of the sequential reaction and the redox-dependent interaction between BphA3 and BphA4, we determined the crystal structures of the productive BphA3-BphA4 complex, and of free BphA3 and BphA4 in all the redox states occurring in the catalytic cycle. The crystal structures of these reaction intermediates demonstrated that each elementary electron transfer induces a series of redox-dependent conformational changes in BphA3 and BphA4, which regulate the interaction between them. In addition, the conformational changes induced by the preceding electron transfer seem to induce the next electron transfer. The interplay of electron transfer and induced conformational changes seems to be critical to the sequential electron-transfer reaction from NADH to BphA3.
-===Crystal structure of BphA3 (oxidized form)===
+Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin.,Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T J Mol Biol. 2007 Oct 19;373(2):382-400. Epub 2007 Aug 19. PMID:17850818<ref>PMID:17850818</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2e4p" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17850818}}, adds the Publication Abstract to the page
+*[[Ferredoxin 3D structures|Ferredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17850818 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17850818}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-E4P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E4P OCA].
+[[Category: Pseudomonas sp]]
+[[Category: Fukuda M]]
-==Reference==
+[[Category: Ishida T]]
-Molecular mechanism of the redox-dependent interaction between NADH-dependent ferredoxin reductase and Rieske-type [2Fe-2S] ferredoxin., Senda M, Kishigami S, Kimura S, Fukuda M, Ishida T, Senda T, J Mol Biol. 2007 Oct 19;373(2):382-400. Epub 2007 Aug 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17850818 17850818]
+[[Category: Kimura S]]
+[[Category: Kishigami S]]
-Crystallization and preliminary X-ray analysis of the Rieske-type [2Fe-2S] ferredoxin component of biphenyl dioxygenase from Pseudomonas sp. strain KKS102., Senda M, Kimura S, Kishigami S, Senda T, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Jun 1;62(Pt, 6):590-2. Epub 2006 May 31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16754990 16754990]
+[[Category: Senda M]]
-[[Category: Pseudomonas sp.]]
+[[Category: Senda T]]
-[[Category: Single protein]]
-[[Category: Fukuda, M.]]
-[[Category: Ishida, T.]]
-[[Category: Kimura, S.]]
-[[Category: Kishigami, S.]]
-[[Category: Senda, M.]]
-[[Category: Senda, T.]]
-[[Category: Electron transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:57:57 2008''