1dap

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[[Image:1dap.gif|left|200px]]<br /><applet load="1dap" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dap, resolution 2.2&Aring;" />
 
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'''C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+'''<br />
 
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==Overview==
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==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+==
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Diaminopimelate dehydrogenase catalyzes the NADPH-dependent reduction of, ammonia and L-2-amino-6-ketopimelate to form meso-diaminopimelate, the, direct precursor of L-lysine in the bacterial lysine biosynthetic pathway., Since mammals lack this metabolic pathway inhibitors of enzymes in this, pathway may be useful as antibiotics or herbicides. Diaminopimelate, dehydrogenase catalyzes the only oxidative deamination of an amino acid of, D configuration and must additionally distinguish between two chiral amino, acid centers on the same symmetric substrate. The Corynebacterium, glutamicum enzyme has been cloned, expressed in Escherichia coli, and, purified to homogeneity using standard biochemical procedures [Reddy, S., G., Scapin, G., &amp; Blanchard, J. S. (1996) Proteins: Structure, Funct., Genet. 25, 514-516]. The three-dimensional structure of the binary complex, of diaminopimelate dehydrogenase with NADP+ has been solved using multiple, isomorphous replacement procedures and noncrystallographic symmetry, averaging. The resulting model has been refined against 2.2 A diffraction, data to a conventional crystallographic R-factor of 17.0%. Diaminopimelate, dehydrogenase is a homodimer of structurally not identical subunits. Each, subunit is composed of three domains. The N-terminal domain contains a, modified dinucleotide binding domain, or Rossman fold (six central, beta-strands in a 213456 topology surrounded by five alpha-helices). The, second domain contains two alpha-helices and three beta-strands. This, domain is referred to as the dimerization domain, since it is involved in, forming the monomer--monomer interface of the dimer. The third or, C-terminal domain is composed of six beta-strands and five alpha-helices., The relative position of the N- and C-terminal domain in the two monomers, is different, defining an open and a closed conformation that may, represent the enzyme's binding and active state, respectively. In both, monomers the nucleotide is bound in an extended conformation across the, C-terminal portion of the beta-sheet of the Rossman fold, with its C4, facing the C-terminal domain. In the closed conformer two molecules of, acetate have been refined in this region, and we postulate that they, define the DAP binding site. The structure of diaminopimelate, dehydrogenase shows interesting similarities to the structure of glutamate, dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W., Rob, A., &amp;, Stillmann, T.J. (1992a) J. Mol. Biol. 228, 662-671] and leucine, dehydrogenase [Baker, P.J., Turnbull, A.P., Sedelnikova, S.E., Stillman, T. J., &amp; Rice, D. W. (1995) Structure 3, 693-705] and also resembles the, structure of dihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., &amp; Sacchettini, J. C. (1995) Biochemistry 34, 3502-3512], the enzyme, immediately preceding it in the diaminopimelic acid/lysine biosynthetic, pathway.
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<StructureSection load='1dap' size='340' side='right'caption='[[1dap]], [[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'>[[1dap]] 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=1DAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DAP FirstGlance]. <br>
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1DAP 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 <scene name='pdbligand=ACT:'>ACT</scene> and <scene name='pdbligand=NDP:'>NDP</scene> 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] Known structural/functional Sites: <scene name='pdbsite=ACE:Acetate+Binding+Site+In+Second+Molecule'>ACE</scene>, <scene name='pdbsite=N1:Nadp++Binding+Site+In+First+Molecule'>N1</scene> and <scene name='pdbsite=N2:Nadp++Binding+Site+In+Second+Molecule'>N2</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DAP 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=ACT:ACETATE+ION'>ACT</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=1dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dap OCA], [https://pdbe.org/1dap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dap RCSB], [https://www.ebi.ac.uk/pdbsum/1dap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dap ProSAT]</span></td></tr>
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Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum., Scapin G, Reddy SG, Blanchard JS, Biochemistry. 1996 Oct 22;35(42):13540-51. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8885833 8885833]
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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/1dap_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=1dap 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: 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: ACT]]
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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: lysine biosynthesis]]
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[[Category: nadp]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 09:35:22 2008''
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Current revision

C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+

PDB ID 1dap

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