PDBsum entry 1drv

Oxidoreductase

PDB id: 1drv

Contents

Protein chain

270 a.a. *

Ligands

A3D

Waters ×69

* Residue conservation analysis

PDB id:

1drv

Name:

Oxidoreductase

Title:

Escherichia coli dhpr/acnadh complex

Structure:

Dihydrodipicolinate reductase. Chain: a. Synonym: dhpr, dapb. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: dapb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å R-factor: 0.191

Authors:

S.G.Reddy,G.Scapin,J.S.Blanchard

Key ref:

S.G.Reddy et al. (1996). Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. Biochemistry, 35, 13294-13302. PubMed id: 8873595 DOI: 10.1021/bi9615809

Date:

28-Jun-96 Release date: 27-Jan-97

Protein chain

P04036  (DAPB_ECOLI) -  4-hydroxy-tetrahydrodipicolinate reductase from Escherichia coli (strain K12)

Seq: 273 a.a.

Struc: 270 a.a.

Enzyme reactions

• Enzyme class: E.C.1.17.1.8 - 4-hydroxy-tetrahydrodipicolinate reductase.
• Reaction:
  1. (S)-2,3,4,5-tetrahydrodipicolinate + NAD⁺ + H2O = (2S,4S)-4- hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + H⁺
  2. (S)-2,3,4,5-tetrahydrodipicolinate + NADP⁺ + H2O = (2S,4S)-4- hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H⁺

(S)-2,3,4,5-tetrahydrodipicolinate + NAD(+) + H2O (Bound ligand (Het Group name = A3D) matches with 95.56% similarity) = (2S,4S)-4- hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + H(+)

(S)-2,3,4,5-tetrahydrodipicolinate + NADP(+) + H2O (Bound ligand (Het Group name = A3D) matches with 87.76% similarity) = (2S,4S)-4- hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi9615809

Biochemistry 35:13294-13302 (1996)

PubMed id: 8873595

Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes.

S.G.Reddy, G.Scapin, J.S.Blanchard.

ABSTRACT

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.