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| - | [[Image:1dap.gif|left|200px]] | |
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| - | {{Structure
| + | ==C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+== |
| - | |PDB= 1dap |SIZE=350|CAPTION= <scene name='initialview01'>1dap</scene>, resolution 2.2Å
| + | <StructureSection load='1dap' size='340' side='right'caption='[[1dap]], [[Resolution|resolution]] 2.20Å' scene=''> |
| - | |SITE= <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>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene> | + | <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> |
| - | |ACTIVITY= <span class='plainlinks'>[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] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | |GENE= DAPDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1718 Corynebacterium glutamicum])
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dap OCA], [http://www.ebi.ac.uk/pdbsum/1dap PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dap RCSB]</span>
| + | == Function == |
| - | }}
| + | [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> |
| - | | + | == Evolutionary Conservation == |
| - | '''C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/da/1dap_consurf.spt"</scriptWhenChecked> |
| - | 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., & 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., & 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., & Rice, D. W. (1995) Structure 3, 693-705] and also resembles the structure of dihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., & Sacchettini, J. C. (1995) Biochemistry 34, 3502-3512], the enzyme immediately preceding it in the diaminopimelic acid/lysine biosynthetic pathway.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1DAP 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=1DAP OCA].
| + | </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]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference== | + | == References == |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/8885833 8885833]
| + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Corynebacterium glutamicum]] | | [[Category: Corynebacterium glutamicum]] |
| - | [[Category: Diaminopimelate dehydrogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Blanchard JS]] |
| - | [[Category: Blanchard, J S.]] | + | [[Category: Reddy SG]] |
| - | [[Category: Reddy, S G.]] | + | [[Category: Scapin G]] |
| - | [[Category: Scapin, G.]] | + | |
| - | [[Category: asymmetric dimer]]
| + | |
| - | [[Category: d-amino acid dehydrogenase]]
| + | |
| - | [[Category: dehydrogenase]]
| + | |
| - | [[Category: lysine biosynthesis]]
| + | |
| - | [[Category: nadp]]
| + | |
| - | [[Category: oxidoreductase]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:37:51 2008''
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