Experimental Data Snapshot

  • Resolution: 1.40 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Crystal Structure of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase.

Inagaki, E.Ohshima, N.Takahashi, H.Kuroishi, C.Yokoyama, S.Tahirov, T.H.

(2006) J Mol Biol 362: 490

  • DOI: https://doi.org/10.1016/j.jmb.2006.07.048
  • Primary Citation of Related Structures:  
    1UZB, 2BHP, 2BHQ, 2BJA, 2BJK, 2IY6

  • PubMed Abstract: 

    Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDh) plays an important role in the metabolic pathway from proline to glutamate. It irreversibly catalyzes the oxidation of glutamate-gamma-semialdehyde, the product of the non-enzymatic hydrolysis of Delta(1)-pyrroline-5-carboxylate, into glutamate with the reduction of NAD(+) into NADH. We have confirmed the P5CDh activity of the Thermus thermophilus protein TT0033 (TtP5CDh), and determined the crystal structure of the enzyme in the ligand-free form at 1.4 A resolution. To investigate the structural basis of TtP5CDh function, the TtP5CDh structures with NAD(+), with NADH, and with its product glutamate were determined at 1.8 A, 1.9 A, and 1.4 A resolution, respectively. The solved structures suggest an overall view of the P5CDh catalytic mechanism and provide insights into the P5CDh deficiencies in the case of the human type II hyperprolinemia.

  • Organizational Affiliation

    RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
516Thermus thermophilus HB8Mutation(s): 0 
Find proteins for P83849 (Thermus thermophilus)
Explore P83849 
Go to UniProtKB:  P83849
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83849
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.40 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.285α = 90
b = 102.285β = 90
c = 279.283γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-11
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description