1smk: Difference between revisions

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-[[Image:1smk.gif|left|200px]]
- {{Structure
+==Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures==
-|PDB= 1smk |SIZE=350|CAPTION= <scene name='initialview01'>1smk</scene>, resolution 2.5&Aring;
+<StructureSection load='1smk' size='340' side='right'caption='[[1smk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>
+<table><tr><td colspan='2'>[[1smk]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrullus_lanatus Citrullus lanatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SMK FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+</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>
-|GENE=
+<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>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1smk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1smk OCA], [https://pdbe.org/1smk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1smk RCSB], [https://www.ebi.ac.uk/pdbsum/1smk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1smk ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1smk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1smk OCA], [http://www.ebi.ac.uk/pdbsum/1smk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1smk RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/MDHG_CITLA MDHG_CITLA]
+== 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/sm/1smk_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=1smk ConSurf].
+<div style="clear:both"></div>
-'''Mature and translocatable forms of glyoxysomal malate dehydrogenase have different activities and stabilities but similar crystal structures'''
+==See Also==
+*[[Malate Dehydrogenase 3D structures|Malate Dehydrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Many organelle enzymes coded for by nuclear genes have N-terminal sequences, which directs them into the organelle (precursor) and are removed upon import (mature). The experiments described below characterize the differences between the precursor and mature forms of watermelon glyoxysomal malate dehydrogenase. Using recombinant protein methods, the precursor (p-gMDH) and mature (gMDH) forms were purified to homogeneity using Ni2+-NTA affinity chromatography. Gel filtration and dynamic light scattering have shown both gMDH and p-gMDH to be dimers in solution with p-gMDH having a correspondingly higher molecular weight. p-gMDH also exhibited a smaller translational diffusion coefficient (D(t)) at temperatures between 4 and 32 degrees C resulting from the extra amino acids on the N-terminal. Differential scanning calorimetry described marked differences in the unfolding properties of the two proteins with p-gMDH showing additional temperature dependent transitions. In addition, some differences were found in the steady state kinetic constants and the pH dependence of the K(m) for oxaloacetate. Both the organelle-precursor and the mature form of this glyoxysomal enzyme were crystallized under identical conditions. The crystal structure of p-gMDH, the first structure of a cleavable and translocatable protein, was solved to a resolution of 2.55 A. GMDH is the first glyoxysomal MDH structure and was solved to a resolution of 2.50 A. A comparison of the two structures shows that there are few visible tertiary or quaternary structural differences between corresponding elements of p-gMDH, gMDH and other MDHs. Maps from both the mature and translocatable proteins lack significant electron density prior to G44. While no portion of the translocation sequences from either monomer in the biological dimer was visible, all of the other solution properties indicated measurable effects of the additional residues at the N-terminal.
-==About this Structure==
-SMK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Citrullus_lanatus Citrullus lanatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SMK OCA].
-==Reference==
-Organelle and translocatable forms of glyoxysomal malate dehydrogenase. The effect of the N-terminal presequence., Cox B, Chit MM, Weaver T, Gietl C, Bailey J, Bell E, Banaszak L, FEBS J. 2005 Feb;272(3):643-54. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15670147 15670147]
 [[Category: Citrullus lanatus]]
-[[Category: Malate dehydrogenase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Bailey J]]
-[[Category: Bailey, J.]]
+[[Category: Banaszak L]]
-[[Category: Banaszak, L.]]
+[[Category: Bell E]]
-[[Category: Bell, E.]]
+[[Category: Chit MM]]
-[[Category: Chit, M M.]]
+[[Category: Cox B]]
-[[Category: Cox, B.]]
+[[Category: Gietl C]]
-[[Category: Gietl, C.]]
+[[Category: Weaver T]]
-[[Category: Weaver, T.]]
-[[Category: glyoxylate bypass]]
-[[Category: glyoxysome]]
-[[Category: nad]]
-[[Category: tricarboxylic cycle]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:44:06 2008''