1TJ0

Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) co-crystallized with L-lactate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors

Zhang, M.White, T.A.Schuermann, J.P.Baban, B.A.Becker, D.F.Tanner, J.J.

(2004) Biochemistry 43: 12539-12548

  • DOI: https://doi.org/10.1021/bi048737e
  • Primary Citation of Related Structures:  
    1TIW, 1TJ0, 1TJ1, 1TJ2

  • PubMed Abstract: 

    Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the flavin-dependent oxidation of proline to Delta(1)-pyrroline-5-carboxylate. Here we present a structure-based study of the PRODH active site of the multifunctional Escherichia coli proline utilization A (PutA) protein using X-ray crystallography, enzyme kinetic measurements, and site-directed mutagenesis. Structures of the PutA PRODH domain complexed with competitive inhibitors acetate (K(i) = 30 mM), L-lactate (K(i) = 1 mM), and L-tetrahydro-2-furoic acid (L-THFA, K(i) = 0.2 mM) have been determined to high-resolution limits of 2.1-2.0 A. The discovery of acetate as a competitive inhibitor suggests that the carboxyl is the minimum functional group recognized by the active site, and the structures show how the enzyme exploits hydrogen-bonding and nonpolar interactions to optimize affinity for the substrate. The PRODH/L-THFA complex is the first structure of PRODH with a five-membered ring proline analogue bound in the active site and thus provides new insights into substrate recognition and the catalytic mechanism. The ring of L-THFA is nearly parallel to the middle ring of the FAD isoalloxazine, with the inhibitor C5 atom 3.3 A from the FAD N5. This geometry suggests direct hydride transfer as a plausible mechanism. Mutation of conserved active site residue Leu432 to Pro caused a 5-fold decrease in k(cat) and a severe loss in thermostability. These changes are consistent with the location of Leu432 in the hydrophobic core near residues that directly contact FAD. Our results suggest that the molecular basis for increased plasma proline levels in schizophrenic subjects carrying the missense mutation L441P is due to decreased stability of human PRODH2.


  • Organizational Affiliation

    Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional putA protein602Escherichia coliMutation(s): 0 
Gene Names: PUTAPOAAB1014
EC: 1.5.99.8 (PDB Primary Data), 1.2.1.88 (UniProt), 1.5.5.2 (UniProt)
UniProt
Find proteins for P09546 (Escherichia coli (strain K12))
Explore P09546 
Go to UniProtKB:  P09546
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09546
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.244α = 90
b = 139.431β = 90
c = 146.051γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2013-11-13
    Changes: Non-polymer description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection