3dap

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[[Image:3dap.gif|left|200px]]<br />
 
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<applet load="3dap" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="3dap, resolution 2.2&Aring;" />
 
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'''C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE'''<br />
 
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==Overview==
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==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE==
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The three-dimensional structures of Corynebacterium glutamicum, diaminopimelate dehydrogenase as a binary complex with the substrate, meso-diaminopimelate (meso-DAP) and a ternary complex with NADP+ and an, isoxazoline inhibitor [Abbot, S.D., Lane-Bell, P., Kanwar, P.S.S., and, Vederas, J. C. (1994) J. Am. Chem. Soc. 116, 6513-6520] have been solved, and refined against X-ray diffraction data to 2.2 A. Diaminopimelate, dehydrogenase is a homodimer of approximately 35,000 molecular weight, subunits and is the only dehydrogenase present in the bacterial, diaminopimelate/lysine biosynthetic pathway. Inhibitors of the enzymes of, L-lysine biosynthesis have been proposed as potential antibiotics or, herbicides, since mammals lack this metabolic pathway. Diaminopimelate, dehydrogenase catalyzes ... [[http://ispc.weizmann.ac.il/pmbin/getpm?9521647 (full description)]]
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<StructureSection load='3dap' size='340' side='right'caption='[[3dap]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[3dap]] is a 2 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=3DAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DAP FirstGlance]. <br>
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3DAP is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]] with NDP and DA3 as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/Diaminopimelate_dehydrogenase Diaminopimelate dehydrogenase]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.16 1.4.1.16]]. Structure known Active Sites: INH, N1 and N2. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3DAP OCA]].
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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]] 2.2&#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=DA3:(2S,5,S)-2-AMINO-3-(3-CARBOXY-2-ISOXAZOLIN-5-YL)PROPANOIC+ACID'>DA3</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
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==Reference==
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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=3dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dap OCA], [https://pdbe.org/3dap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dap RCSB], [https://www.ebi.ac.uk/pdbsum/3dap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dap ProSAT]</span></td></tr>
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Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase., Scapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS, Biochemistry. 1998 Mar 10;37(10):3278-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9521647 9521647]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DAPDH_CORGL DAPDH_CORGL] Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD(+) only poorly since the activity observed in the presence of NAD(+) is about 3% of that with NADP(+).<ref>PMID:8865347</ref> <ref>PMID:8865347</ref>
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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/da/3dap_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=3dap ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Corynebacterium glutamicum]]
[[Category: Corynebacterium glutamicum]]
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[[Category: Diaminopimelate dehydrogenase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Blanchard JS]]
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[[Category: Blanchard, J.S.]]
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[[Category: Cirilli M]]
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[[Category: Cirilli, M.]]
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[[Category: Gao Y]]
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[[Category: Gao, Y.]]
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[[Category: Reddy SG]]
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[[Category: Reddy, S.G.]]
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[[Category: Scapin G]]
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[[Category: Scapin, G.]]
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[[Category: Vederas JC]]
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[[Category: Vederas, J.C.]]
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[[Category: DA3]]
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[[Category: NDP]]
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[[Category: asymmetric dimer]]
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[[Category: d-amino acid dehydrogenase]]
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[[Category: dehydrogenase]]
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[[Category: inhibitor]]
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[[Category: lysine biosynthesis]]
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[[Category: nadp]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 17:45:08 2007''
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Current revision

C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE

PDB ID 3dap

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