1gv0: Difference between revisions

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-[[Image:1gv0.png|left|200px]]
-<!--
+==Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases==
-The line below this paragraph, containing "STRUCTURE_1gv0", creates the "Structure Box" on the page.
+<StructureSection load='1gv0' size='340' side='right'caption='[[1gv0]], [[Resolution|resolution]] 2.50&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'>[[1gv0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlorobaculum_tepidum Chlorobaculum tepidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GV0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GV0 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-{{STRUCTURE_1gv0|  PDB=1gv0  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gv0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gv0 OCA], [https://pdbe.org/1gv0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gv0 RCSB], [https://www.ebi.ac.uk/pdbsum/1gv0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gv0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MDH_CHLTE MDH_CHLTE] Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487]
+== 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/gv/1gv0_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=1gv0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of four malate dehydrogenases (MDH) from thermophilic and mesophilic phototropic bacteria have been determined by X-ray crystallography and the corresponding structures compared. In contrast to the dimeric quaternary structure of most MDHs, these MDHs are tetramers and are structurally related to tetrameric malate dehydrogenases from Archaea and to lactate dehydrogenases. The tetramers are dimers of dimers, where the structures of each subunit and the dimers are similar to the dimeric malate dehydrogenases. The difference in optimal growth temperature of the corresponding organisms is relatively small, ranging from 32 to 55 degrees C. Nevertheless, on the basis of the four crystal structures, a number of factors that are likely to contribute to the relative thermostability in the present series have been identified. It appears from the results obtained, that the difference in thermostability between MDH from the mesophilic Chlorobium vibrioforme on one hand and from the moderate thermophile Chlorobium tepidum on the other hand is mainly due to the presence of polar residues that form additional hydrogen bonds within each subunit. Furthermore, for the even more thermostable Chloroflexus aurantiacus MDH, the use of charged residues to form additional ionic interactions across the dimer-dimer interface is favored. This enzyme has a favorable intercalation of His-Trp as well as additional aromatic contacts at the monomer-monomer interface in each dimer. A structural alignment of tetrameric and dimeric prokaryotic MDHs reveal that structural elements that differ among dimeric and tetrameric MDHs are located in a few loop regions.
-===STRUCTURAL BASIS FOR THERMOPHILIC PROTEIN STABILITY: STRUCTURES OF THERMOPHILIC AND MESOPHILIC MALATE DEHYDROGENASES===
+Structural basis for thermophilic protein stability: structures of thermophilic and mesophilic malate dehydrogenases.,Dalhus B, Saarinen M, Sauer UH, Eklund P, Johansson K, Karlsson A, Ramaswamy S, Bjork A, Synstad B, Naterstad K, Sirevag R, Eklund H J Mol Biol. 2002 May 3;318(3):707-21. PMID:12054817<ref>PMID:12054817</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_12054817}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1gv0" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12054817 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_12054817}}
-==About this Structure==
-[[1gv0]] is a 2 chain structure of [[Malate dehydrogenase]] with sequence from [http://en.wikipedia.org/wiki/Chlorobaculum_tepidum Chlorobaculum tepidum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GV0 OCA].
 ==See Also==
-*[[Malate dehydrogenase]]
+*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:12054817</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Chlorobaculum tepidum]]
-[[Category: Malate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Bjork, A.]]
+[[Category: Bjork A]]
-[[Category: Dalhus, B.]]
+[[Category: Dalhus B]]
-[[Category: Eklund, H.]]
+[[Category: Eklund H]]
-[[Category: Eklund, P.]]
+[[Category: Eklund P]]
-[[Category: Johansson, K.]]
+[[Category: Johansson K]]
-[[Category: Karlsson, A.]]
+[[Category: Karlsson A]]
-[[Category: Naterstad, K.]]
+[[Category: Naterstad K]]
-[[Category: Ramaswamy, S.]]
+[[Category: Ramaswamy S]]
-[[Category: Sarinen, M.]]
+[[Category: Sarinen M]]
-[[Category: Sauer, U H.]]
+[[Category: Sauer UH]]
-[[Category: Sirevag, R.]]
+[[Category: Sirevag R]]
-[[Category: Synstad, B.]]
+[[Category: Synstad B]]
-[[Category: Dehydrogenase]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-[[Category: Tricarboxylic acid]]