1j4a: Difference between revisions

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-[[Image:1j4a.jpg|left|200px]]<br /><applet load="1j4a" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1j4a, resolution 1.9&Aring;" />
-'''INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS'''<br />
-==Overview==
+==INSIGHTS INTO DOMAIN CLOSURE, SUBSTRATE SPECIFICITY AND CATALYSIS OF D-LACTATE DEHYDROGENASE FROM LACTOBACILLUS BULGARICUS==
-NAD-dependent Lactobacillus bulgaricus D-Lactate dehydrogenase (D-LDHb), catalyses the reversible conversion of pyruvate into D-lactate. Crystals, of D-LDHb complexed with NADH were grown and X-ray data collected to 2.2, A. The structure of D-LDHb was solved by molecular replacement using the, dimeric Lactobacillus helveticus D-LDH as a model and was refined to an, R-factor of 20.7%. The two subunits of the enzyme display strong asymmetry, due to different crystal environments. The opening angles of the two, catalytic domains with respect to the core coenzyme binding domains differ, by 16 degrees. Subunit A is in an "open" conformation typical for a, dehydrogenase apo enzyme and subunit B is "closed". The NADH-binding site, in subunit A is only 30% occupied, while in subunit B it is fully occupied, and there is a sulphate ion in the substrate-binding pocket. A pyruvate, molecule has been modelled in the active site and its orientation is in, agreement with existing kinetic and structural data. On domain closure, a, cluster of hydrophobic residues packs tightly around the methyl group of, the modelled pyruvate molecule. At least three residues from this cluster, govern the substrate specificity. Substrate binding itself contributes to, the stabilisation of domain closure and activation of the enzyme. In, pyruvate reduction, D-LDH can adapt another protonated residue, a lysine, residue, to accomplish the role of the acid catalyst His296. Required, lowering of the lysine pK(a) value is explained on the basis of the H296K, mutant structure.
+<StructureSection load='1j4a' size='340' side='right'caption='[[1j4a]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1j4a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus Lactobacillus delbrueckii subsp. bulgaricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J4A 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1j4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j4a OCA], [https://pdbe.org/1j4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j4a RCSB], [https://www.ebi.ac.uk/pdbsum/1j4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j4a ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LDHD_LACDA LDHD_LACDA]
+== 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/j4/1j4a_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=1j4a ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-J4A is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_delbrueckii_subsp._bulgaricus Lactobacillus delbrueckii subsp. bulgaricus] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/D-lactate_dehydrogenase D-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.28 1.1.1.28] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J4A OCA].
+*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Domain closure, substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus., Razeto A, Kochhar S, Hottinger H, Dauter M, Wilson KS, Lamzin VS, J Mol Biol. 2002 Apr 19;318(1):109-19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12054772 12054772]
-[[Category: D-lactate dehydrogenase]]
 [[Category: Lactobacillus delbrueckii subsp. bulgaricus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Dauter, M.]]
+[[Category: Dauter M]]
-[[Category: Hottinger, H.]]
+[[Category: Hottinger H]]
-[[Category: Kochhar, S.]]
+[[Category: Kochhar S]]
-[[Category: Lamzin, V.S.]]
+[[Category: Lamzin VS]]
-[[Category: Razeto, A.]]
+[[Category: Razeto A]]
-[[Category: Wilson, K.S.]]
+[[Category: Wilson KS]]
-[[Category: SO4]]
-[[Category: nad-dependent dehydrogenase]]
-[[Category: reversible interconversion of pyruvate into d-lactate]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 17:55:32 2007''