1dih: Difference between revisions

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-[[Image:1dih.gif|left|200px]]
- {{Structure
+==THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE==
-|PDB= 1dih |SIZE=350|CAPTION= <scene name='initialview01'>1dih</scene>, resolution 2.2&Aring;
+<StructureSection load='1dih' size='340' side='right'caption='[[1dih]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=NDP:NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE'>NDP</scene>
+<table><tr><td colspan='2'>[[1dih]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DIH FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Dihydrodipicolinate_reductase Dihydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.26 1.3.1.26]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=1dih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dih OCA], [https://pdbe.org/1dih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dih RCSB], [https://www.ebi.ac.uk/pdbsum/1dih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dih ProSAT]</span></td></tr>
+</table>
-'''THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE'''
+== Function ==
+[https://www.uniprot.org/uniprot/DAPB_ECOLI DAPB_ECOLI] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. Can use both NADH and NADPH as a reductant, with NADH being twice as effective as NADPH.<ref>PMID:7893644</ref> <ref>PMID:20503968</ref>
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-Dihydrodipicolinate reductase is an enzyme found in bacteria and higher plants involved in the biosynthesis of diaminopimelic acid and lysine. Because these pathways are unique to bacteria and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds. The three-dimensional structure of Escherichia coli dihydrodipicolinate reductase, complexed with NADPH, has been determined and refined to a crystallographic R-factor of 18.6% with diffraction data to 2.2 A resolution. The refined model contains the complete protein chain, the cofactor NADPH, and 55 water molecules. The enzyme is composed of two domains. The dinucleotide binding domain has a central seven-stranded parallel beta-sheet surrounded by four alpha-helices, with the cofactor binding site located at the carboxy-terminal edge of the sheet. The second domain contains four beta-strands and two alpha-helices that form an open mixed beta-sandwich. A possible binding site for dihydrodipicolinate has been identified in this second domain, about 12 A away from the dinucleotide binding site. This would imply that the protein must undergo some conformational change in order to perform catalysis. In the crystal, the native enzyme is a homotetramer generated by a 222 crystallographic axis. Implications of the tetrameric structure for the enzyme function are presented. Dihydrodipicolinate reductase uses both NADH and NADPH as cofactors, and analysis of its cofactor binding site allows for a molecular understanding of the enzyme's dual specificity.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/di/1dih_consurf.spt"</scriptWhenChecked>
-DIH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIH OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase., Scapin G, Blanchard JS, Sacchettini JC, Biochemistry. 1995 Mar 21;34(11):3502-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7893645 7893645]
+</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=1dih ConSurf].
-[[Category: Dihydrodipicolinate reductase]]
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Blanchard, J S.]]
+[[Category: Blanchard JS]]
-[[Category: Sacchettini, J C.]]
+[[Category: Sacchettini JC]]
-[[Category: Scapin, G.]]
+[[Category: Scapin G]]
-[[Category: NDP]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:38:58 2008''