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1bmd

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[[Image:1bmd.gif|left|200px]]<br /><applet load="1bmd" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1bmd, resolution 1.9&Aring;" />
 
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'''DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGSTROMS CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE THERMOPHILIC BACTERIUM THERMUS FLAVUS'''<br />
 
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==Overview==
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==DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGSTROMS CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE THERMOPHILIC BACTERIUM THERMUS FLAVUS==
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A binary complex of malate dehydrogenase from the thermophilic bacterium Thermus flavus (tMDH) with NADH has been crystallized from poly(ethylene glycol) 3500, pH 8.5, yielding diffraction-quality crystals in space group P2(1)2(1)2(1). The structure was solved at 1.9-A resolution using molecular replacement and refined to an R factor of 15.8% with good geometry. The primary sequence of tMDH is 55% identical to that of cytoplasmic malate dehydrogenase (cMDH) [Birktoft, J. J., Rhodes, G., &amp; Banaszak, L. J. (1989) Biochemistry 28, 6065-6081], and overall their three-dimensional structures are very similar. Like cMDH, tMDH crystallized as a dimer with one coenzyme bound per subunit. The coenzyme binds in the extended conformation, and most of the interactions with enzyme are similar to those in cMDH. In tMDH, small local conformational changes are caused by the replacement of a glutamic acid for the aspartic acid involved in hydrogen bonding to the adenine ribose of NADH. Comparison of tMDH with cMDH reveals that both tMDH subunits more closely resemble the B subunit of cMDH which therefore is the more likely representative of the solution conformation. While cMDH is inactivated at temperatures above about 50 degrees C, tMDH is fully active at 90 degrees C. On the basis of the X-ray crystal structure, a number of factors have been identified which are likely to contribute to the relative thermostability of tMDH compared to cMDH. The most striking of the differences involves the introduction of four ion pairs per monomer. All of these ion pairs are solvent-accessible. Three of these ion pairs are located in the dimer interface, Glu27-Lys31, Glu57-Lys168, and Glu57-Arg229, and one ion pair, Glu275-Arg149, is at the domain interface within each subunit. Additionally, we observe incorporation of additional alanines into alpha-helices of tMDH and, in one instance, incorporation of an aspartate that functions as a counterchange to an alpha-helix dipole. The possible contributions of these and other factors to protein thermostability in tMDH are discussed.
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<StructureSection load='1bmd' size='340' side='right'caption='[[1bmd]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1bmd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BMD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BMD FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bmd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bmd OCA], [https://pdbe.org/1bmd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bmd RCSB], [https://www.ebi.ac.uk/pdbsum/1bmd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bmd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MDH_THETH MDH_THETH] Catalyzes the reversible oxidation of malate to oxaloacetate.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/1bmd_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1bmd ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1BMD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BMD OCA].
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*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus., Kelly CA, Nishiyama M, Ohnishi Y, Beppu T, Birktoft JJ, Biochemistry. 1993 Apr 20;32(15):3913-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8471603 8471603]
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[[Category: Large Structures]]
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[[Category: Malate dehydrogenase]]
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[[Category: Single protein]]
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[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Birktoft, J J.]]
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[[Category: Birktoft JJ]]
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[[Category: Kelly, C A.]]
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[[Category: Kelly CA]]
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[[Category: NAD]]
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[[Category: oxidoreductase(choh(d)-nad+(a))]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:56:53 2008''
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Current revision

DETERMINANTS OF PROTEIN THERMOSTABILITY OBSERVED IN THE 1.9 ANGSTROMS CRYSTAL STRUCTURE OF MALATE DEHYDROGENASE FROM THE THERMOPHILIC BACTERIUM THERMUS FLAVUS

PDB ID 1bmd

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