Crystal Structure of Yeast ALDH4A1

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

Starting Model: experimental
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Structural Studies of Yeast Delta (1)-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State.

Pemberton, T.A.Srivastava, D.Sanyal, N.Henzl, M.T.Becker, D.F.Tanner, J.J.

(2014) Biochemistry 53: 1350-1359

  • DOI: https://doi.org/10.1021/bi500048b
  • Primary Citation of Related Structures:  
    4OE4, 4OE5, 4OE6

  • PubMed Abstract: 

    The proline catabolic enzyme Δ(1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) catalyzes the NAD(+)-dependent oxidation of γ-glutamate semialdehyde to l-glutamate. In Saccharomyces cerevisiae, ALDH4A1 is encoded by the PUT2 gene and known as Put2p. Here we report the steady-state kinetic parameters of the purified recombinant enzyme, two crystal structures of Put2p, and the determination of the oligomeric state and quaternary structure from small-angle X-ray scattering and sedimentation velocity. Using Δ(1)-pyrroline-5-carboxylate as the substrate, catalytic parameters kcat and Km were determined to be 1.5 s(-1) and 104 μM, respectively, with a catalytic efficiency of 14000 M(-1) s(-1). Although Put2p exhibits the expected aldehyde dehydrogenase superfamily fold, a large portion of the active site is disordered in the crystal structure. Electron density for the 23-residue aldehyde substrate-binding loop is absent, implying substantial conformational flexibility in solution. We furthermore report a new crystal form of human ALDH4A1 (42% identical to Put2p) that also shows disorder in this loop. The crystal structures provide evidence of multiple active site conformations in the substrate-free form of the enzyme, which is consistent with a conformational selection mechanism of substrate binding. We also show that Put2p forms a trimer-of-dimers hexamer in solution. This result is unexpected because human ALDH4A1 is dimeric, whereas some bacterial ALDH4A1s are hexameric. Thus, global sequence identity and domain of life are poor predictors of the oligomeric states of ALDH4A1. Mutation of a single Trp residue that forms knob-in-hole interactions across the dimer-dimer interface abrogates hexamer formation, suggesting that this residue is the center of a protein-protein association hot spot.

  • Organizational Affiliation

    Department of Chemistry, University of Missouri-Columbia , Columbia, Missouri 65211, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
A, B
580Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUT2YHR037W
Find proteins for P07275 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07275 
Go to UniProtKB:  P07275
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07275
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.032α = 90
b = 109.032β = 90
c = 181.246γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2014-02-19 
  • Deposition Author(s): Tanner, J.J.

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-19
    Type: Initial release
  • Version 1.1: 2014-03-19
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description