1drv
From Proteopedia
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|PDB= 1drv |SIZE=350|CAPTION= <scene name='initialview01'>1drv</scene>, resolution 2.2Å | |PDB= 1drv |SIZE=350|CAPTION= <scene name='initialview01'>1drv</scene>, resolution 2.2Å | ||
|SITE= <scene name='pdbsite=BIN:Dinucleotide+Binding+Site'>BIN</scene> | |SITE= <scene name='pdbsite=BIN:Dinucleotide+Binding+Site'>BIN</scene> | ||
| - | |LIGAND= <scene name='pdbligand=A3D:3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE'>A3D</scene> | + | |LIGAND= <scene name='pdbligand=A3D:3-ACETYLPYRIDINE+ADENINE+DINUCLEOTIDE'>A3D</scene> |
| - | |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] | + | |ACTIVITY= <span class='plainlinks'>[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] </span> |
|GENE= DAPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= DAPB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1drv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1drv OCA], [http://www.ebi.ac.uk/pdbsum/1drv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1drv RCSB]</span> | ||
}} | }} | ||
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[[Category: Reddy, S G.]] | [[Category: Reddy, S G.]] | ||
[[Category: Scapin, G.]] | [[Category: Scapin, G.]] | ||
| - | [[Category: A3D]] | ||
[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:47:28 2008'' |
Revision as of 16:47, 30 March 2008
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| , resolution 2.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | |||||||
| Ligands: | |||||||
| Gene: | DAPB (Escherichia coli) | ||||||
| Activity: | Dihydrodipicolinate reductase, with EC number 1.3.1.26 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
ESCHERICHIA COLI DHPR/ACNADH COMPLEX
Overview
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.
About this Structure
1DRV is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
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:8873595
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