1drv

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[[Image:1drv.gif|left|200px]]
 
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{{Structure
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==ESCHERICHIA COLI DHPR/ACNADH COMPLEX==
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|PDB= 1drv |SIZE=350|CAPTION= <scene name='initialview01'>1drv</scene>, resolution 2.2&Aring;
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<StructureSection load='1drv' size='340' side='right'caption='[[1drv]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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|SITE= <scene name='pdbsite=BIN:Dinucleotide+Binding+Site'>BIN</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=A3D:3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE'>A3D</scene>
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<table><tr><td colspan='2'>[[1drv]] 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=1DRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DRV FirstGlance]. <br>
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|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]
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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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|GENE= DAPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3D:3-ACETYLPYRIDINE+ADENINE+DINUCLEOTIDE'>A3D</scene></td></tr>
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}}
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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=1drv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1drv OCA], [https://pdbe.org/1drv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1drv RCSB], [https://www.ebi.ac.uk/pdbsum/1drv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1drv ProSAT]</span></td></tr>
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</table>
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'''ESCHERICHIA COLI DHPR/ACNADH COMPLEX'''
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== Function ==
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[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>
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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E. coli dihydrodipicolinate reductase exhibits unusual nucleotide specificity, with NADH being kinetically twice as effective as NADPH as a reductant as evidenced by their relative V/K values. To investigate the nature of the interactions which determine this specificity, we performed isothermal titration calorimetry to determine the thermodynamic parameters of binding and determined the three-dimensional structures of the corresponding enzyme-nucleotide complexes. The thermodynamic binding parameters for NADPH and NADH were determined to be Kd = 2.12 microM, delta G degree = -7.81 kcal mol-1, delta H degree = -10.98 kcal mol-1, and delta S degree = -10.5 cal mol-1 deg-1 and Kd = 0.46 microM, delta G degree = -8.74 kcal mol-1, delta H degree = -8.93 kcal mol-1, and delta S degree = 0.65 cal mol-1 deg-1, respectively. The structures of DHPR complexed with these nucleotides have been determined at 2.2 A resolution. The 2'-phosphate of NADPH interacts electrostatically with Arg39, while in the NADH complex this interaction is replaced by hydrogen bonds between the 2' and 3' adenosyl ribose hydroxyls and Glu38. Similar studies were also performed with other pyridine nucleotide substrate analogs to determine the contributions of individual groups on the nucleotide to the binding affinity and enthalpic and entropic components of the free energy of binding, delta G degree. Analogs lacking the 2'-phosphate containing homologs. For all analogs, the total binding free energy can be shown to include compensating enthalpic and entropic contributions to the association constants. The entropy contribution appears to play a more important role in the binding of the nonphosphorylated analogs than in the binding of the phosphorylated analogs.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dr/1drv_consurf.spt"</scriptWhenChecked>
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1DRV 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=1DRV OCA].
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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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==Reference==
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</jmolCheckbox>
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Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes., Reddy SG, Scapin G, Blanchard JS, Biochemistry. 1996 Oct 15;35(41):13294-302. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873595 8873595]
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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=1drv ConSurf].
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[[Category: Dihydrodipicolinate reductase]]
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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: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Blanchard, J S.]]
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[[Category: Blanchard JS]]
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[[Category: Reddy, S G.]]
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[[Category: Reddy SG]]
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[[Category: Scapin, G.]]
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[[Category: Scapin G]]
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[[Category: A3D]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:43:18 2008''
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Current revision

ESCHERICHIA COLI DHPR/ACNADH COMPLEX

PDB ID 1drv

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