4O8A

First structure of a proline utilization A proline dehydrogenase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein.

Lee, Y.H.Nadaraia, S.Gu, D.Becker, D.F.Tanner, J.J.

(2003) Nat.Struct.Mol.Biol. 10: 109-114

  • DOI: 10.1038/nsb885
  • Primary Citation of Related Structures:  1K87
  • Also Cited By: 4O8A

  • PubMed Abstract: 
  • The PutA flavoprotein from Escherichia coli plays multiple roles in proline catabolism by functioning as a membrane-associated bi-functional enzyme and a transcriptional repressor of proline utilization genes. The human homolog of the PutA proline de ...

    The PutA flavoprotein from Escherichia coli plays multiple roles in proline catabolism by functioning as a membrane-associated bi-functional enzyme and a transcriptional repressor of proline utilization genes. The human homolog of the PutA proline dehydrogenase (PRODH) domain is critical in p53-mediated apoptosis and schizophrenia. Here we report the crystal structure of a 669-residue truncated form of PutA that shows both PRODH and DNA-binding activities, representing the first structure of a PutA protein and a PRODH enzyme from any organism. The structure is a domain-swapped dimer with each subunit comprising three domains: a helical dimerization arm, a 120-residue domain containing a three-helix bundle similar to that in the helix-turn-helix superfamily of DNA-binding proteins and a beta/alpha-barrel PRODH domain with a bound lactate inhibitor. Analysis of the structure provides insight into the mechanism of proline oxidation to pyrroline-5-carboxylate, and functional studies of a mutant protein suggest that the DNA-binding domain is located within the N-terminal 261 residues of E. coli PutA.


    Related Citations: 
    • Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein.
      Lee, Y.H.,Nadaraia, S.,Gu, D.,Becker, D.F.,Tanner, J.J.
      (2003) Nat.Struct.Mol.Biol. 10: 109


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein PutA
A
687Escherichia coli (strain K12)Gene Names: putA (poaA)
EC: 1.2.1.88, 1.5.5.2
Find proteins for P09546 (Escherichia coli (strain K12))
Go to UniProtKB:  P09546
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
2OP
Query on 2OP

Download SDF File 
Download CCD File 
A
(2S)-2-HYDROXYPROPANOIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.620α = 90.00
b = 140.430β = 90.00
c = 145.850γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-12-26 
  • Released Date: 2014-01-15 
  • Deposition Author(s): Tanner, J.J.
  • This entry supersedes: 1K87

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release