2GR9

Crystal structure of P5CR complexed with NADH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


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.Biol. 359: 1364-1377

  • DOI: 10.1016/j.jmb.2006.04.053
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrroline-5-carboxylate reductase 1
A, B, C, D, E
277Homo sapiensMutation(s): 0 
Gene Names: PYCR1
EC: 1.5.1.2
Find proteins for P32322 (Homo sapiens)
Go to Gene View: PYCR1
Go to UniProtKB:  P32322
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU
Download SDF File 
Download CCD File 
A, B, C, D, E
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
NAI
Query on NAI
Download SDF File 
Download CCD File 
A, B, C, D, E
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 208.182α = 90.00
b = 122.642β = 122.03
c = 120.708γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
CrystalCleardata reduction
CNSphasing
CrystalCleardata collection

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2013-11-06
    Type: Non-polymer description