2GER | pdb_00002ger

Crystal Structure and Oxidative Mechanism of Human Pyrroline-5-carboxylate Reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.261 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2GER

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human pyrroline-5-carboxylate reductase

Meng, Z.Lou, Z.Liu, Z.Li, M.Zhao, X.Bartlam, M.Rao, Z.

(2006) J Mol Biology 359: 1364-1377

  • DOI: https://doi.org/10.1016/j.jmb.2006.04.053
  • Primary Citation Related Structures: 
    2GER, 2GR9, 2GRA

  • PubMed Abstract: 

    Pyrroline-5-carboxylate reductase (P5CR) is a universal housekeeping enzyme that catalyzes the reduction of Delta(1)-pyrroline-5-carboxylate (P5C) to proline using NAD(P)H as the cofactor. The enzymatic cycle between P5C and proline is very important for the regulation of amino acid metabolism, intracellular redox potential, and apoptosis. Here, we present the 2.8 Angstroms resolution structure of the P5CR apo enzyme, its 3.1 Angstroms resolution ternary complex with NAD(P)H and substrate-analog. The refined structures demonstrate a decameric architecture with five homodimer subunits and ten catalytic sites arranged around a peripheral circular groove. Mutagenesis and kinetic studies reveal the pivotal roles of the dinucleotide-binding Rossmann motif and residue Glu221 in the human enzyme. Human P5CR is thermostable and the crystals were grown at 37 degrees C. The enzyme is implicated in oxidation of the anti-tumor drug thioproline.


  • Organizational Affiliation
    • Tsinghua-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 168.15 kDa 
  • Atom Count: 10,768 
  • Modeled Residue Count: 1,384 
  • Deposited Residue Count: 1,605 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pyrroline-5-carboxylate reductase 1
A, B, C, D, E
321Homo sapiensMutation(s): 0 
EC: 1.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P32322 (Homo sapiens)
Explore P32322 
Go to UniProtKB:  P32322
PHAROS:  P32322
GTEx:  ENSG00000183010 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32322
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.261 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.607α = 90
b = 123.805β = 121.76
c = 120.79γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data reduction
SHELXmodel building
CNSrefinement
HKL-2000data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary