Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.57 kDa 
• Atom Count: 3801 
• Modelled Residue Count: 459 
• Deposited Residue Count: 602 
• Unique protein chains: 1

1TIW

Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with L-Tetrahydro-2-furoic acid

• PDB DOI: 10.2210/pdb1TIW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-02 Released: 2004-10-26 
• Deposition Author(s): Tanner, J.J., Zhang, M., White, T.A., Schuermann, J.P., Baban, B.A., Becker, D.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

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

• PubMed: 15449943 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional putA protein	A	602	Escherichia coli	Mutation(s): 0  Gene Names: putA, poaA, b1014 EC: 1.5.99.8 (PDB Primary Data), 1.5.5.2 (UniProt), 1.2.1.88 (UniProt)
UniProt
Find proteins for P09546 (Escherichia coli (strain K12)) Explore P09546  Go to UniProtKB:  P09546

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
TFB	C [auth A]	TETRAHYDROFURAN-2-CARBOXYLIC ACID C5 H8 O3 UJJLJRQIPMGXEZ-BYPYZUCNSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TFB	Binding MOAD:  1TIW	Ki: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.253 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.588	α = 90
b = 141.358	β = 90
c = 145.897	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-02 
• Released Date: 2004-10-26 
Deposition Author(s): Tanner, J.J., Zhang, M., White, T.A., Schuermann, J.P., Baban, B.A., Becker, D.F.

Revision History  

• 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, Version format compliance