1ldc: Difference between revisions

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-{{Seed}}
-[[Image:1ldc.png|left|200px]]
-<!--
+==X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE==
-The line below this paragraph, containing "STRUCTURE_1ldc", creates the "Structure Box" on the page.
+<StructureSection load='1ldc' size='340' side='right'caption='[[1ldc]], [[Resolution|resolution]] 2.90&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'>[[1ldc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LDC 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]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
-{{STRUCTURE_1ldc|  PDB=1ldc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ldc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ldc OCA], [https://pdbe.org/1ldc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ldc RCSB], [https://www.ebi.ac.uk/pdbsum/1ldc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ldc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CYB2_YEAST CYB2_YEAST]
+== 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/ld/1ldc_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=1ldc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Flavocytochrome b2 is a flavohemo enzyme localized in the intermembrane space of yeast mitochondria, where it catalyzes the electron transfer from its substrate, L-lactate, to cytochrome c. We have obtained crystals of a flavocytochrome b2 mutant, Y143F, which are isostructural with those of the native recombinant enzyme [Tegoni, M., &amp; Cambillau, C. (1994) Protein Sci.3, 303-314]. These crystals were grown under similar conditions to those used to obtain the recombinant enzyme, but in the presence of phenyl lactate or lactate. We report here on the structural analysis of the two complexes of flavocytochrome b2 with the reaction products at 2.9 A resolution. In both structures, the Phe143 phenyl ring keeps the same position as that of the phenolic ring of Tyr143 in both the native recombinant and in the native wild-type enzymes. The product of the reaction, phenyl pyruvate or pyruvate, is present at the active site of both subunits, and not only in subunit 2 as observed in the wild-type structure [Xia, Z.-X., &amp; Mathews, F.S. (1990) J. Mol. Biol. 212, 837-863]. The number of interactions between the FMN and the heme domain is considerably lower in the Y143F mutant than in the native proteins. The latter finding strongly supports the hypothesis that the main role of Tyr143 in the native proteins. The latter findings strongly supports the hypothesis that the main role of Tyr143 in the native protein probably consists in establishing a hydrogen bond with the heme [Xia, Z.-X., &amp; Mathews, F.S. (1990) J. Mol. Biol. 212, 837-863]. This interaction appears to be essential for the two domains to approach each other suitably so that the intramolecular electron transfer can occur.
-===X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE===
+X-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate.,Tegoni M, Begotti S, Cambillau C Biochemistry. 1995 Aug 8;34(31):9840-50. PMID:7632684<ref>PMID:7632684</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ldc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_7632684}}, adds the Publication Abstract to the page
+*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 7632684 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_7632684}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-LDC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDC OCA].
-==Reference==
-X-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate., Tegoni M, Begotti S, Cambillau C, Biochemistry. 1995 Aug 8;34(31):9840-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7632684 7632684]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Cambillau C]]
-[[Category: Cambillau, C.]]
+[[Category: Tegoni M]]
-[[Category: Tegoni, M.]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 12:29:54 2008''