1lth: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==T AND R STATES IN THE CRYSTALS OF BACTERIAL L-LACTATE DEHYDROGENASE REVEAL THE MECHANISM FOR ALLOSTERIC CONTROL==
-<StructureSection load='1lth' size='340' side='right' caption='[[1lth]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1lth' size='340' side='right'caption='[[1lth]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1lth]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum_biovar_longum Bifidobacterium longum biovar longum]. The June 2008 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Lactate Dehydrogenase''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_6 10.2210/rcsb_pdb/mom_2008_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LTH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1lth]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum Bifidobacterium longum subsp. longum]. The June 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Lactate Dehydrogenase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_6 10.2210/rcsb_pdb/mom_2008_6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LTH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LTH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene></td></tr>
+</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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BIFIDOBACTERIUM LONGUM LDH GENE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1679 Bifidobacterium longum biovar Longum])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=OXM:OXAMIC+ACID'>OXM</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=1lth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lth OCA], [https://pdbe.org/1lth PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lth RCSB], [https://www.ebi.ac.uk/pdbsum/1lth PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lth ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1lth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lth OCA], [http://pdbe.org/1lth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lth RCSB], [http://www.ebi.ac.uk/pdbsum/1lth PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LDH2_BIFL2 LDH2_BIFL2] Catalyzes the conversion of lactate to pyruvate.[HAMAP-Rule:MF_00488]
 == 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/lt/1lth_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lt/1lth_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1lth ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of L-lactate dehydrogenase from Bifidobacterium longum, determined to 2.5 A resolution, contains a regular 1:1 complex of T- and R-state tetramers. A comparison of these two structures within the same crystal lattice and kinetical characterization of the T-R transition in solution provide an explanation for the molecular mechanism of allosteric activation. Substrate affinity is controlled by helix sliding between subunits which is triggered by the binding of the activator, fructose 1,6-bisphosphate. The proposed mechanism can explain activation by chemical modification and mutagenesis, as well as suggesting why vertebrate counterparts are not allosteric.
-T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control.,Iwata S, Kamata K, Yoshida S, Minowa T, Ohta T Nat Struct Biol. 1994 Mar;1(3):176-85. PMID:7656036<ref>PMID:7656036</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1lth" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Lactate Dehydrogenase|Lactate Dehydrogenase]]
+*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bifidobacterium longum biovar longum]]
+[[Category: Bifidobacterium longum subsp. longum]]
-[[Category: L-lactate dehydrogenase]]
 [[Category: Lactate Dehydrogenase]]
+[[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Iwata, S]]
+[[Category: Iwata S]]
-[[Category: Ohta, T]]
+[[Category: Ohta T]]
-[[Category: Allosteric enzyme]]
-[[Category: Oxidoreductase]]