1DIH

THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase.

Scapin, G.Blanchard, J.S.Sacchettini, J.C.

(1995) Biochemistry 34: 3502-3512

  • DOI: 10.1021/bi00011a003
  • Primary Citation of Related Structures:  
    1DIH

  • PubMed Abstract: 
  • Dihydrodipicolinate reductase is an enzyme found in bacteria and higher plants involved in the biosynthesis of diaminopimelic acid and lysine. Because these pathways are unique to bacteria and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds ...

    Dihydrodipicolinate reductase is an enzyme found in bacteria and higher plants involved in the biosynthesis of diaminopimelic acid and lysine. Because these pathways are unique to bacteria and plants, they may represent attractive targets for new antimicrobial or herbicidal compounds. The three-dimensional structure of Escherichia coli dihydrodipicolinate reductase, complexed with NADPH, has been determined and refined to a crystallographic R-factor of 18.6% with diffraction data to 2.2 A resolution. The refined model contains the complete protein chain, the cofactor NADPH, and 55 water molecules. The enzyme is composed of two domains. The dinucleotide binding domain has a central seven-stranded parallel beta-sheet surrounded by four alpha-helices, with the cofactor binding site located at the carboxy-terminal edge of the sheet. The second domain contains four beta-strands and two alpha-helices that form an open mixed beta-sandwich. A possible binding site for dihydrodipicolinate has been identified in this second domain, about 12 A away from the dinucleotide binding site. This would imply that the protein must undergo some conformational change in order to perform catalysis. In the crystal, the native enzyme is a homotetramer generated by a 222 crystallographic axis. Implications of the tetrameric structure for the enzyme function are presented. Dihydrodipicolinate reductase uses both NADH and NADPH as cofactors, and analysis of its cofactor binding site allows for a molecular understanding of the enzyme's dual specificity.


    Related Citations: 
    • Expression, Purification and Characterization of E. Coli Dihydrodipicolinate Reductase
      Reddy, S., Sacchettini, J.C., Blanchard, J.S.
      (1995) Biochemistry 34: 3492

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDRODIPICOLINATE REDUCTASEA273Escherichia coliMutation(s): 0 
EC: 1.3.1.26 (PDB Primary Data), 1.17.1.8 (UniProt)
UniProt
Find proteins for P04036 (Escherichia coli (strain K12))
Explore P04036 
Go to UniProtKB:  P04036
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NDP Binding MOAD:  1DIH Kd: 2120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.187 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.7α = 90
b = 81.2β = 90
c = 94.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-09-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description