2b0t: Difference between revisions

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-[[Image:2b0t.gif|left|200px]]
- {{Structure
+==Structure of Monomeric NADP Isocitrate dehydrogenase==
-|PDB= 2b0t |SIZE=350|CAPTION= <scene name='initialview01'>2b0t</scene>, resolution 1.75&Aring;
+<StructureSection load='2b0t' size='340' side='right'caption='[[2b0t]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
+<table><tr><td colspan='2'>[[2b0t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B0T FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NADP(+)) Isocitrate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2b0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b0t OCA], [https://pdbe.org/2b0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b0t RCSB], [https://www.ebi.ac.uk/pdbsum/2b0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b0t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/IDH_CORGL IDH_CORGL]
+== 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/b0/2b0t_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=2b0t ConSurf].
+<div style="clear:both"></div>
-'''Structure of Monomeric NADP Isocitrate dehydrogenase'''
+==See Also==
+*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Both monomeric and dimeric NADP+-dependent isocitrate dehydrogenase (IDH) belong to the metal-dependent beta-decarboxylating dehydrogenase family and catalyze the oxidative decarboxylation from 2R,3S-isocitrate to yield 2-oxoglutarate, CO2, and NADPH. It is important to solve the structures of IDHs from various species to correlate with its function and evolutionary significance. So far, only two crystal structures of substrate/cofactor-bound (isocitrate/NADP) NADP+-dependent monomeric IDH from Azotobacter vinelandii (AvIDH) have been solved. Herein, we report for the first time the substrate/cofactor-free structure of a monomeric NADP+-dependent IDH from Corynebacterium glutamicum (CgIDH) in the presence of Mg2+. The 1.75 A structure of CgIDH-Mg2+ showed a distinct open conformation in contrast to the closed conformation of AvIDH-isocitrate/NADP+ complexes. Fluorescence studies on CgIDH in the presence of isocitrate/or NADP+ suggest the presence of low energy barrier conformers. In CgIDH, the amino acid residues corresponding to the Escherichia coli IDH phosphorylation-loop are alpha-helical compared with the more flexible random-coil region in the E. coli protein where IDH activation is controlled by phosphorylation. This more structured region supports the idea that activation of CgIDH is not controlled by phosphorylation. Monomeric NADP+-specific IDHs have been identified from about 50 different bacterial species, such as proteobacteria, actinobacteria, and planctomycetes, whereas, dimeric NADP+-dependent IDHs are diversified in both prokaryotes and eukaryotes. We have constructed a phylogenetic tree based on amino acid sequences of all bacterial monomeric NADP+-dependent IDHs and also another one with specifically chosen species which either contains both monomeric and dimeric NADP+-dependent IDHs or have monomeric NADP+-dependent, as well as NAD+-dependent IDHs. This is done to examine evolutionary relationships.
-==About this Structure==
-B0T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B0T OCA].
-==Reference==
-Substrate-free structure of a monomeric NADP isocitrate dehydrogenase: an open conformation phylogenetic relationship of isocitrate dehydrogenase., Imabayashi F, Aich S, Prasad L, Delbaere LT, Proteins. 2006 Apr 1;63(1):100-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16416443 16416443]
 [[Category: Corynebacterium glutamicum]]
-[[Category: Isocitrate dehydrogenase (NADP(+))]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Aich S]]
-[[Category: Aich, S.]]
+[[Category: Delbaere LT]]
-[[Category: Delbaere, L T.]]
+[[Category: Imabayashi F]]
-[[Category: Imabayashi, F.]]
+[[Category: Prasad L]]
-[[Category: Prasad, L.]]
-[[Category: MG]]
-[[Category: idh]]
-[[Category: monomeric]]
-[[Category: nadp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:56:15 2008''