1mld: Difference between revisions

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New page: left|200px<br /><applet load="1mld" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mld, resolution 1.83Å" /> '''REFINED STRUCTURE OF...
 
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[[Image:1mld.gif|left|200px]]<br /><applet load="1mld" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1mld, resolution 1.83&Aring;" />
'''REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES'''<br />


==Overview==
==REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES==
The crystal structure of mitochondrial malate dehydrogenase from porcine, heart contains four identical subunits in the asymmetric unit of a, monoclinic cell. Although the molecule functions as a dimer in solution, it exists as a tetramer with 222 point symmetry in the crystal. The, crystallographic refinement was facilitated in the early stages by using, weak symmetry restraints and molecular dynamics. The R-factor including, X-ray data to 1.83-A resolution was 21.1%. The final root mean square, deviation from canonical values is 0.015 A for bond lengths and 3.2, degrees for bond angles. The resulting model of the tetramer includes, independent coordinates for each of the four subunits allowing an internal, check on the accuracy of the model. The crystalline mitochondrial malate, dehydrogenase tetramer has been analyzed to determine the surface areas, lost at different subunit-subunit interfaces. The results show that the, interface with the largest surface area is the same one found in cytosolic, malate dehydrogenase. Each of the subunits contains a bound citrate, molecule in the active site permitting the elaboration of a model for, substrate binding which agrees with that found for the crystalline enzyme, from Escherichia coli. The environment of the N-terminal region of the, crystallographic model has been studied because the functional protein is, produced from a precursor. This precursor form has an additional 24, residues which are involved in mitochondrial targeting and, possibly, translocation. The crystallographic model of mitochondrial malate, dehydrogenase has been compared with its cytosolic counterpart from, porcine heart and two prokaryotic enzymes. Small but significant, differences have been found in the polar versus nonpolar accessible, surface areas between the mitochondrial and cytosolic enzymes. Using least, squares methods, four different malate dehydrogenases have been, superimposed and their consensus structure has been determined. An amino, acid sequence alignment based on the crystallographic structures describes, all the conserved positions. The consensus active site of these, dicarboxylic acid dehydrogenases is derived from the least squares, comparison.
<StructureSection load='1mld' size='340' side='right'caption='[[1mld]], [[Resolution|resolution]] 1.83&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1mld]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. The October 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Citric Acid Cycle''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_10 10.2210/rcsb_pdb/mom_2012_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MLD 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]] 1.83&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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=1mld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mld OCA], [https://pdbe.org/1mld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mld RCSB], [https://www.ebi.ac.uk/pdbsum/1mld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mld ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MDHM_PIG MDHM_PIG]
== 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/ml/1mld_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=1mld ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1MLD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with CIT 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MLD OCA].
*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Refined crystal structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases., Gleason WB, Fu Z, Birktoft J, Banaszak L, Biochemistry. 1994 Mar 1;33(8):2078-88. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8117664 8117664]
[[Category: Citric Acid Cycle]]
[[Category: Malate dehydrogenase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
[[Category: Banaszak, L.J.]]
[[Category: Banaszak LJ]]
[[Category: Birktoft, J.J.]]
[[Category: Birktoft JJ]]
[[Category: Fu, Z.]]
[[Category: Fu Z]]
[[Category: Gleason, W.B.]]
[[Category: Gleason WB]]
[[Category: CIT]]
[[Category: oxidoreductase(nad(a)-choh(d))]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:30:08 2007''

Latest revision as of 10:45, 14 February 2024

REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASESREFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES

Structural highlights

1mld is a 4 chain structure with sequence from Sus scrofa. The October 2012 RCSB PDB Molecule of the Month feature on Citric Acid Cycle by David Goodsell is 10.2210/rcsb_pdb/mom_2012_10. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.83Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MDHM_PIG

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1mld, resolution 1.83Å

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