Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Work: 0.180 

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

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

(1996) Biochemistry 35: 13294-13302

  • DOI: https://doi.org/10.1021/bi9615809
  • Primary Citation of Related Structures:  
    1DRU, 1DRV, 1DRW

  • PubMed 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.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIHYDRODIPICOLINATE REDUCTASE273Escherichia coliMutation(s): 0 
Gene Names: DAPB
Find proteins for P04036 (Escherichia coli (strain K12))
Explore P04036 
Go to UniProtKB:  P04036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04036
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NHD

Download Ideal Coordinates CCD File 
C21 H26 N6 O15 P2
Binding Affinity Annotations 
IDSourceBinding Affinity
NHD Binding MOAD:  1DRW Kd: 1480 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Work: 0.180 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.6α = 90
b = 81.7β = 90
c = 93.8γ = 90
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description