3ITG

Structure the proline utilization A proline dehydrogenase domain (PutA86-630) inactivated with N-propargylglycine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of the proline utilization a proline dehydrogenase domain inactivated by N-propargylglycine provides insight into conformational changes induced by substrate binding and flavin reduction.

Srivastava, D.Zhu, W.Johnson, W.H.Whitman, C.P.Becker, D.F.Tanner, J.J.

(2010) Biochemistry 49: 560-569

  • DOI: 10.1021/bi901717s

  • PubMed Abstract: 
  • Proline utilization A (PutA) from Escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. Previous s ...

    Proline utilization A (PutA) from Escherichia coli is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. Previous studies have shown that the binding of proline in the proline dehydrogenase (PRODH) active site and subsequent reduction of the FAD trigger global conformational changes that enhance PutA-membrane affinity. These events cause PutA to switch from its repressor to its enzymatic role, but the mechanism by which this signal is propagated from the active site to the distal membrane-binding domain is largely unknown. Here, it is shown that N-propargylglycine irreversibly inactivates PutA by covalently linking the flavin N(5) atom to the epsilon-amino of Lys329. Furthermore, inactivation locks PutA into a conformation that may mimic the proline-reduced, membrane-associated form. The 2.15 A resolution structure of the inactivated PRODH domain suggests that the initial events involved in broadcasting the reduced flavin state to the distal membrane-binding domain include major reorganization of the flavin ribityl chain, severe (35 degrees ) butterfly bending of the isoalloxazine ring, and disruption of an electrostatic network involving the flavin N(5) atom, Arg431, and Asp370. The structure also provides information about conformational changes associated with substrate binding. This analysis suggests that the active site is incompletely assembled in the absence of the substrate, and the binding of proline draws together conserved residues in helix 8 and the beta1-alphal loop to complete the active site.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional protein putA
A, B
602Escherichia 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDA
Query on FDA

Download SDF File 
Download CCD File 
A, B
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYX
Query on LYX
A, B
L-PEPTIDE LINKINGC30 H52 N9 O19 P3 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.193 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 127.480α = 90.00
b = 133.360β = 90.00
c = 133.640γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
MOSFLMdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
SCALAdata scaling
SCALAdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-28 
  • Released Date: 2010-01-12 
  • Deposition Author(s): Tanner, J.J.

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance