8DKQ

Minimal PutA proline dehydrogenase domain (design #2) complexed with 2-(Furan-2-yl)acetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-based engineering of minimal proline dehydrogenase domains for inhibitor discovery.

Bogner, A.N.Ji, J.Tanner, J.J.

(2022) Protein Eng Des Sel 35

  • DOI: https://doi.org/10.1093/protein/gzac016
  • Primary Citation of Related Structures:  
    8DKO, 8DKP, 8DKQ

  • PubMed Abstract: 

    Proline dehydrogenase (PRODH) catalyzes the FAD-dependent oxidation of l-proline to Δ1-pyrroline-5-carboxylate and is a target for inhibitor discovery because of its importance in cancer cell metabolism. Because human PRODH is challenging to purify, the PRODH domains of the bacterial bifunctional enzyme proline utilization A (PutA) have been used for inhibitor development. These systems have limitations due to large polypeptide chain length, conformational flexibility and the presence of domains unrelated to PRODH activity. Herein, we report the engineering of minimal PRODH domains for inhibitor discovery. The best designs contain one-third of the 1233-residue PutA from Sinorhizobium meliloti and include a linker that replaces the PutA α-domain. The minimal PRODHs exhibit near wild-type enzymatic activity and are susceptible to known inhibitors and inactivators. Crystal structures of minimal PRODHs inhibited by S-(-)-tetrahydro-2-furoic acid and 2-(furan-2-yl)acetic acid were determined at 1.23 and 1.72 Å resolution. Minimal PRODHs should be useful in chemical probe discovery.


  • Organizational Affiliation

    Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional protein PutA
A, B
396Sinorhizobium meliloti SM11Mutation(s): 0 
Gene Names: putASM11_chr0102
EC: 1.5.5.2 (PDB Primary Data), 1.2.1.88 (PDB Primary Data)
UniProt
Find proteins for F7X6I3 (Sinorhizobium meliloti (strain SM11))
Explore F7X6I3 
Go to UniProtKB:  F7X6I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7X6I3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.967α = 104.07
b = 55.291β = 100.37
c = 76.092γ = 108.67
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM132640

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection