Crystal Structure of delta1-piperideine-2-carboxylate reductase from Pseudomonas syringae complexed with NADPH and pyrrole-2-carboxylate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

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Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction

Goto, M.Muramatsu, H.Mihara, H.Kurihara, T.Esaki, N.Omi, R.Miyahara, I.Hirotsu, K.

(2005) J Biol Chem 280: 40875-40884

  • DOI: https://doi.org/10.1074/jbc.M507399200
  • Primary Citation of Related Structures:  
    1WTJ, 2CWF, 2CWH

  • PubMed Abstract: 

    Delta(1)-Piperideine-2-carboxylate/Delta(1)-pyrroline-2-carboxylate reductase from Pseudomonas syringae pv. tomato belongs to a novel sub-class in a large family of NAD(P)H-dependent oxidoreductases distinct from the conventional MDH/LDH superfamily characterized by the Rossmann fold. We have determined the structures of the following three forms of the enzyme: the unliganded form, the complex with NADPH, and the complex with NADPH and pyrrole-2-carboxylate at 1.55-, 1.8-, and 1.7-A resolutions, respectively. The enzyme exists as a dimer, and the subunit consists of three domains; domain I, domain II (NADPH binding domain), and domain III. The core of the NADPH binding domain consists of a seven-stranded predominantly antiparallel beta-sheet fold (which we named SESAS) that is characteristic of the new oxidoreductase family. The enzyme preference for NADPH over NADH is explained by the cofactor binding site architecture. A comparison of the overall structures revealed that the mobile domains I and III change their conformations to produce the catalytic form. This conformational change plays important roles in substrate recognition and the catalytic process. The active site structure of the catalytic form made it possible to identify the catalytic Asp:Ser:His triad and investigate the catalytic mechanism from a stereochemical point of view.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
delta1-piperideine-2-carboxylate reductase
A, B
343Pseudomonas syringae pv. tomatoMutation(s): 0 
Gene Names: dpkA
EC: 1.5.1
Find proteins for Q4U331 (Pseudomonas syringae pv. tomato)
Explore Q4U331 
Go to UniProtKB:  Q4U331
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4U331
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.972α = 90
b = 68.874β = 90
c = 179.333γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations