1jrz: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1jrz.png|left|200px]]
-<!--
+==Crystal structure of Arg402Tyr mutant flavocytochrome c3 from Shewanella frigidimarina==
-The line below this paragraph, containing "STRUCTURE_1jrz", creates the "Structure Box" on the page.
+<StructureSection load='1jrz' size='340' side='right'caption='[[1jrz]], [[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'>[[1jrz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JRZ 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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUM:FUMARIC+ACID'>FUM</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1jrz|  PDB=1jrz  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jrz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jrz OCA], [https://pdbe.org/1jrz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jrz RCSB], [https://www.ebi.ac.uk/pdbsum/1jrz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jrz ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/FRDA_SHEFR FRDA_SHEFR] Catalyzes fumarate reduction using artificial electron donors such as methyl viologen. The physiological reductant is unknown, but evidence indicates that flavocytochrome c participates in electron transfer from formate to fumarate and possibly also to trimethylamine oxide (TMAO). This enzyme is essentially unidirectional.
+== 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/jr/1jrz_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=1jrz ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+There is now overwhelming evidence supporting a common mechanism for fumarate reduction in the respiratory fumarate reductases. The X-ray structures of substrate-bound forms of these enzymes indicate that the substrate is well positioned to accept a hydride from FAD and a proton from an arginine side chain. Recent work on the enzyme from Shewanella frigidimarina [Doherty, M. K., Pealing, S. L., Miles, C. S., Moysey, R., Taylor, P., Walkinshaw, M. D., Reid, G. A., and Chapman, S. K. (2000) Biochemistry 39, 10695-10701] has strengthened the assignment of an arginine (Arg402) as the proton donor in fumarate reduction. Here we describe the crystallographic and kinetic analyses of the R402A, R402K, and R402Y mutant forms of the Shewanella enzyme. The crystal structure of the R402A mutant (2.0 A resolution) shows it to be virtually identical to the wild-type enzyme, apart from the fact that a water molecule occupies the position previously taken by part of the guanidine group of R402. Although structurally similar to the wild-type enzyme, the R402A mutant is inactive under all the conditions that were studied. This implies that a water molecule, in this position in the active site, cannot function as the proton donor for fumarate reduction. In contrast to the R402A mutation, both the R402K and R402Y mutant enzymes are active. Although this activity was at a very low level (at pH 7.2 some 10(4)-fold lower than that for the wild type), it does imply that both lysine and tyrosine can fulfill the role of an active site proton donor, albeit very poorly. The crystal structures of the R402K and R402Y mutant enzymes (2.0 A resolution) show that distances from the lysine and tyrosine side chains to the nearest carbon atom of fumarate are approximately 3.5 A, clearly permitting proton transfer. The combined results from mutagenesis, crystallographic, and kinetic studies provide formidable evidence that R402 acts as both a Lewis acid (stabilizing the build-up of negative charge upon hydride transfer from FAD to fumarate) and a Bronsted acid (donating the proton to the substrate to complete the formation of succinate).
-===Crystal structure of Arg402Tyr mutant flavocytochrome c3 from Shewanella frigidimarina===
+Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase.,Mowat CG, Moysey R, Miles CS, Leys D, Doherty MK, Taylor P, Walkinshaw MD, Reid GA, Chapman SK Biochemistry. 2001 Oct 16;40(41):12292-8. PMID:11591148<ref>PMID:11591148</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1jrz" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11591148}}, adds the Publication Abstract to the page
+*[[Flavocytochrome 3D structures|Flavocytochrome 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 11591148 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11591148}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-JRZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_frigidimarina Shewanella frigidimarina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JRZ OCA].
-==Reference==
-Kinetic and crystallographic analysis of the key active site acid/base arginine in a soluble fumarate reductase., Mowat CG, Moysey R, Miles CS, Leys D, Doherty MK, Taylor P, Walkinshaw MD, Reid GA, Chapman SK, Biochemistry. 2001 Oct 16;40(41):12292-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11591148 11591148]
 [[Category: Shewanella frigidimarina]]
-[[Category: Single protein]]
+[[Category: Chapman SK]]
-[[Category: Succinate dehydrogenase]]
+[[Category: Doherty MK]]
-[[Category: Chapman, S K.]]
+[[Category: Leys D]]
-[[Category: Doherty, M K.]]
+[[Category: Miles CS]]
-[[Category: Leys, D.]]
+[[Category: Mowat CG]]
-[[Category: Miles, C S.]]
+[[Category: Moysey R]]
-[[Category: Mowat, C G.]]
+[[Category: Reid GA]]
-[[Category: Moysey, R.]]
+[[Category: Taylor P]]
-[[Category: Reid, G A.]]
+[[Category: Walkinshaw MD]]
-[[Category: Taylor, P.]]
-[[Category: Walkinshaw, M D.]]
-[[Category: Flavocytochrome]]
-[[Category: Fumarate reductase]]
-[[Category: Mutant]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 20:42:52 2008''