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1ldm

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(New page: 200px<br /> <applet load="1ldm" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ldm, resolution 2.1&Aring;" /> '''REFINED CRYSTAL STRU...)
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[[Image:1ldm.gif|left|200px]]<br />
 
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<applet load="1ldm" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ldm, resolution 2.1&Aring;" />
 
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'''REFINED CRYSTAL STRUCTURE OF DOGFISH M4 APO-LACTATE DEHYDROGENASE'''<br />
 
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==Overview==
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==Refined crystal structure of dogfish M4 apo-lactate dehydrogenase==
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The crystal structure of M4 apo-lactate dehydrogenase from the spiny, dogfish (Squalus acanthius) was initially refined by a, constrained-restrained, and subsequently restrained, least-squares, technique. The final structure contained 286 water molecules and two, sulfate ions per subunit and gave an R-factor of 0.202 for difraction data, between 8.0 and 2.0 A resolution. The upper limit for the co-ordinate, accuracy of the atoms was estimated to be 0.25 A. The elements of, secondary structure of the refined protein have not changed from those, described previously, except for the appearance of a one-and-a-half turn, 3(10) helix immediately after beta J. There is also a short segment of, 3(10) helix between beta C and beta D in the part of the chain that, connects the two beta alpha beta alpha beta units of the six-stranded, parallel sheet (residues Tyr83 to Ala87). Examination of the interactions, among the different elements of secondary structure by means of a surface, accessibility algorithm supports the four structural clusters in the, subunit. The first of the two sulfate ions is in the active site and, occupies a cavity near the essential His195. Its nearest protein ligands, are Arg171, Asp168 and Asn140. The second sulfate ion is located near the, P-axis subunit interface. It is liganded by His188 and Arg173. These two, residues are conserved in bacterial lactate dehydrogenase and form part of, the fructose 1,6-bisphosphate effector binding site. Two other data sets, in which one (collected at pH 7.8) or both (collected at pH 6.0) sulfate, ions were replaced by citrate ions were also analyzed. Five cycles of, refinement with respect to the pH 6.0 data (25 to 2.8 A resolution), resulted in an R value of 0.191. Only water molecules occupy the subunit, boundary anion binding site at pH 7.8. The amino acid sequence was found, to be in poor agreement with (2Fobs-Fcalc) electron density maps for the, peptide between residues 207 and 211. The original sequence WNALKE was, replaced by NVASIK. The essential His195 is hydrogen bonded to Asp168 on, one side and Asn140 on the other. The latter residue is part of a turn, that contains the only cis peptide bond of the structure at Pro141. The, "flexible loop" (residues 97 to 123), which folds down over the active, center in ternary complexes of the enzyme with substrate and coenzyme, has, a well-defined structure. Analysis of the environment of Tyr237 suggests, how its chemical modification inhibits the enzyme.
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<StructureSection load='1ldm' size='340' side='right'caption='[[1ldm]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ldm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Squalus_acanthias Squalus acanthias]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LDM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LDM 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]] 2.1&#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>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</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=1ldm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ldm OCA], [https://pdbe.org/1ldm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ldm RCSB], [https://www.ebi.ac.uk/pdbsum/1ldm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ldm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LDHA_SQUAC LDHA_SQUAC]
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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/ld/1ldm_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=1ldm 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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1LDM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with NAD and OXM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LDM OCA].
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*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Refined crystal structure of dogfish M4 apo-lactate dehydrogenase., Abad-Zapatero C, Griffith JP, Sussman JL, Rossmann MG, J Mol Biol. 1987 Dec 5;198(3):445-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3430615 3430615]
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[[Category: Large Structures]]
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[[Category: L-lactate dehydrogenase]]
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[[Category: Squalus acanthias]]
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[[Category: Single protein]]
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[[Category: Griffith JP]]
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[[Category: Griffith, J.P.]]
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[[Category: Rossmann MG]]
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[[Category: Rossmann, M.G.]]
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[[Category: NAD]]
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[[Category: OXM]]
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[[Category: oxidoreductase(choh(d)-nad(a))]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov 8 12:41:24 2007''
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Current revision

Refined crystal structure of dogfish M4 apo-lactate dehydrogenase

PDB ID 1ldm

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