4O8A

First structure of a proline utilization A proline dehydrogenase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


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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 Biol 10: 109-114

  • DOI: 10.1038/nsb885
  • Primary Citation of Related Structures:  
    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 dehydrogenase (PRODH) domain is critical in p53-mediated apoptosis and schizophrenia ...

    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 Biol 10: 109

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional protein PutAA687Escherichia coli K-12Mutation(s): 0 
Gene Names: b1014JW0999poaAputA
EC: 1.5.99.8 (PDB Primary Data), 1.2.1.88 (PDB Primary Data), 1.5.5.2 (UniProt)
UniProt
Find proteins for P09546 (Escherichia coli (strain K12))
Explore P09546 
Go to UniProtKB:  P09546
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
2OP
Query on 2OP

Download Ideal Coordinates CCD File 
C [auth A](2S)-2-HYDROXYPROPANOIC ACID
C3 H6 O3
JVTAAEKCZFNVCJ-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.62α = 90
b = 140.43β = 90
c = 145.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment  



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  (Full details and data files)

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