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==2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)== | |||
<StructureSection load='2j5k' size='340' side='right'caption='[[2j5k]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2j5k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J5K FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2j5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j5k OCA], [https://pdbe.org/2j5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j5k RCSB], [https://www.ebi.ac.uk/pdbsum/2j5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j5k ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MDH_HALMA MDH_HALMA] 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/j5/2j5k_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=2j5k ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Intense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X-ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side-chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side-chains. This suggests that residues with higher pK(a) values are more vulnerable to damage than those with a lower pK(a). However, such a correlation was not found when calculated pK(a) values were inspected. (ii) Acidic side-chains located in the enzymatic active site are the most radiation-sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility. | |||
Specific radiation damage to acidic residues and its relation to their chemical and structural environment.,Fioravanti E, Vellieux FM, Amara P, Madern D, Weik M J Synchrotron Radiat. 2007 Jan;14(Pt 1):84-91. Epub 2006 Dec 15. PMID:17211074<ref>PMID:17211074</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2j5k" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]] | |||
*[[Malate | == References == | ||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: Haloarcula marismortui]] | [[Category: Haloarcula marismortui]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Amara | [[Category: Amara P]] | ||
[[Category: Fioravanti | [[Category: Fioravanti E]] | ||
[[Category: Madern | [[Category: Madern D]] | ||
[[Category: Vellieux | [[Category: Vellieux FMD]] | ||
[[Category: Weik | [[Category: Weik M]] | ||
Latest revision as of 17:35, 13 December 2023
2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)2.0 A resolution structure of the wild type malate dehydrogenase from Haloarcula marismortui (radiation damage series)
Structural highlights
FunctionMDH_HALMA Catalyzes the reversible oxidation of malate to oxaloacetate.[HAMAP-Rule:MF_00487] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedIntense synchrotron radiation produces specific structural and chemical damage to crystalline proteins even at 100 K. Carboxyl groups of acidic residues (Glu, Asp) losing their definition is one of the major effects observed. Here, the susceptibilities to X-ray damage of acidic residues in tetrameric malate dehydrogenase from Haloarcula marismortui are investigated. The marked excess of acidic residues in this halophilic enzyme makes it an ideal target to determine how specific damage to acidic residues is related to their structural and chemical environment. Four conclusions are drawn. (i) Acidic residues interacting with the side-chains of lysine and arginine residues are less affected by radiation damage than those interacting with serine, threonine and tyrosine side-chains. This suggests that residues with higher pK(a) values are more vulnerable to damage than those with a lower pK(a). However, such a correlation was not found when calculated pK(a) values were inspected. (ii) Acidic side-chains located in the enzymatic active site are the most radiation-sensitive ones. (iii) Acidic residues in the internal cavity formed by the four monomers and those involved in crystal contacts appear to be particularly susceptible. (iv) No correlation was found between radiation susceptibility and solvent accessibility. Specific radiation damage to acidic residues and its relation to their chemical and structural environment.,Fioravanti E, Vellieux FM, Amara P, Madern D, Weik M J Synchrotron Radiat. 2007 Jan;14(Pt 1):84-91. Epub 2006 Dec 15. PMID:17211074[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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