1p2e: Difference between revisions

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-{{Seed}}
-[[Image:1p2e.png|left|200px]]
-<!--
+==H61A mutant of flavocytochrome c3==
-The line below this paragraph, containing "STRUCTURE_1p2e", creates the "Structure Box" on the page.
+<StructureSection load='1p2e' size='340' side='right'caption='[[1p2e]], [[Resolution|resolution]] 2.20&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'>[[1p2e]] is a 1 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=1P2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P2E 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <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_1p2e|  PDB=1p2e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p2e OCA], [https://pdbe.org/1p2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p2e RCSB], [https://www.ebi.ac.uk/pdbsum/1p2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p2e 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/p2/1p2e_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=1p2e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An examination of the X-ray structure of the soluble fumarate reductase from Shewanella frigidimarina [Taylor, P., Pealing, S. L., Reid, G. A., Chapman, S. K., and Walkinshaw, M. D. (1999) Nat. Struct. Biol. 6, 1108-1112] shows the presence of four, bis-His-ligated, c-type hemes and one flavin adenine dinucleotide, FAD. The heme groups provide a "molecular wire" for the delivery of electrons to the FAD. Heme IV is closest to the FAD (7.4 A from heme methyl to FAD C7), and His61, a ligand to heme IV, is also close (8.4 A to FAD C7). Electron delivery to the FAD from the heme groups must proceed via heme IV, as hemes I-III are too far from the FAD for feasible electron transfer. To examine the importance of heme IV and its ligation for enzyme function, we have substituted His61 with both methionine and alanine. Here we describe the crystallographic, kinetic, and electrochemical characterization of the H61M and H61A mutant forms of the Shewanella fumarate reductase. The crystal structures of these mutant forms of the enzyme have been determined to 2.1 and 2.2 A resolution, respectively. Substitution of His61 with alanine results in heme IV having only one protein ligand (His86), the sixth coordination position being occupied by an acetate ion derived from the crystal cryoprotectant solution. In the structure of the H61M enzyme, Met61 is found not to ligate the heme iron, a role that is taken by a water molecule. Apart from these features, there are no significant structural alterations as a result of either substitution. Both the H61M-Fcc(3) and H61A-Fcc(3) mutant enzymes are catalytically active but exhibit marked decreases in the value of k(cat) for fumarate reduction with respect to that of the wild type (5- and 10-fold lower, respectively). There is also a significant shift in the pK(a) values for the mutant enzymes, from 7.5 for the wild type to 8.26 for H61M and 9.29 for H61A. The fumarate reductase activity of both mutant enzymes can be recovered to approximately 80% of that seen for the wild type by the addition of exogenous imidazole. In the case of H61A, recovery of activity is also accompanied by a shift of the pK(a) from 9.29 to 7.46 (close, and within experimental error, to that for the wild type). Pre-steady-state kinetic measurements show clearly that rate constants for the fumarate dependent reoxidation of the heme groups are adversely affected by the mutations. The solvent isotope effect for fumarate reduction in the wild-type enzyme has a value of 8.0, indicating that proton delivery is substantially rate limiting. This value falls to 5.6 and 2.2 for the H61M and H61A mutants, respectively, indicating that electron transfer, rather than proton transfer, is becoming more rate-limiting in the mutant enzymes.
-===H61A mutant of flavocytochrome c3===
+Histidine 61: an important heme ligand in the soluble fumarate reductase from Shewanella frigidimarina.,Rothery EL, Mowat CG, Miles CS, Walkinshaw MD, Reid GA, Chapman SK Biochemistry. 2003 Nov 18;42(45):13160-9. PMID:14609326<ref>PMID:14609326</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1p2e" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14609326}}, adds the Publication Abstract to the page
+*[[Flavocytochrome 3D structures|Flavocytochrome 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14609326 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14609326}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-P2E is a 1 chain 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=1P2E OCA].
-==Reference==
-<ref group="xtra">PMID:14609326</ref><references group="xtra"/>
 [[Category: Shewanella frigidimarina]]
-[[Category: Succinate dehydrogenase]]
+[[Category: Chapman SK]]
-[[Category: Chapman, S K.]]
+[[Category: Miles CS]]
-[[Category: Miles, C S.]]
+[[Category: Mowat CG]]
-[[Category: Mowat, C G.]]
+[[Category: Reid GA]]
-[[Category: Reid, G A.]]
+[[Category: Rothery EL]]
-[[Category: Rothery, E L.]]
+[[Category: Walkinshaw MD]]
-[[Category: Walkinshaw, M D.]]
-[[Category: Flavocytochrome c3]]
-[[Category: Fumarate reductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:59:35 2009''