Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR)

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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This is version 1.2 of the entry. See complete history


The structure of Medicago truncatula delta (1)-pyrroline-5-carboxylate reductase provides new insights into regulation of proline biosynthesis in plants.

Ruszkowski, M.Nocek, B.Forlani, G.Dauter, Z.

(2015) Front Plant Sci 6: 869-869

  • DOI: https://doi.org/10.3389/fpls.2015.00869
  • Primary Citation of Related Structures:  
    5BSE, 5BSF, 5BSG, 5BSH

  • PubMed Abstract: 

    The two pathways for proline biosynthesis in higher plants share the last step, the conversion of δ(1)-pyrroline-5-carboxylate (P5C) to L-proline, which is catalyzed by P5C reductase (P5CR, EC with the use of NAD(P)H as a coenzyme. There is increasing amount of evidence to suggest a complex regulation of P5CR activity at the post-translational level, yet the molecular basis of these mechanisms is unknown. Here we report the three-dimensional structure of the P5CR enzyme from the model legume Medicago truncatula (Mt). The crystal structures of unliganded MtP5CR decamer, and its complexes with the products NAD(+), NADP(+), and L-proline were refined using x-ray diffraction data (at 1.7, 1.85, 1.95, and 2.1 Å resolution, respectively). Based on the presented structural data, the coenzyme preference for NADPH over NADH was explained, and NADPH is suggested to be the only coenzyme used by MtP5CR in vivo. Furthermore, the insensitivity of MtP5CR to feed-back inhibition by proline, revealed by enzymatic analysis, was correlated with structural features. Additionally, a mechanism for the modulation of enzyme activity by chloride anions is discussed, as well as the rationale for the possible development of effective enzyme inhibitors.

  • Organizational Affiliation

    Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute Argonne, IL, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrroline-5-carboxylate reductase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
277Medicago truncatulaMutation(s): 0 
Gene Names: MTR_7g090160
Find proteins for G7KRM5 (Medicago truncatula)
Explore G7KRM5 
Go to UniProtKB:  G7KRM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7KRM5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MPO

Download Ideal Coordinates CCD File 
K [auth A],
N [auth C],
T [auth H],
V [auth I],
X [auth J]
C7 H15 N O4 S
Query on CL

Download Ideal Coordinates CCD File 
L [auth A]
M [auth B]
O [auth C]
P [auth D]
Q [auth E]
L [auth A],
M [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
U [auth H],
W [auth I],
Y [auth J]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.8α = 67.9
b = 100.6β = 85.3
c = 101.2γ = 89.3
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2015-12-02
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description