5BSG

Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR) in complex with NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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 1.5.1.2) 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

    Department of Life Science and Biotechnology, University of Ferrara Ferrara, Italy.


Macromolecules
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
EC: 1.5.1.2
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
IA [auth I]
K [auth A]
LA [auth J]
CA [auth G],
FA [auth H],
IA [auth I],
K [auth A],
LA [auth J],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
MPO
Query on MPO

Download Ideal Coordinates CCD File 
AA [auth F]
DA [auth G]
GA [auth H]
JA [auth I]
L [auth A]
AA [auth F],
DA [auth G],
GA [auth H],
JA [auth I],
L [auth A],
MA [auth J],
O [auth B],
R [auth C],
U [auth D],
X [auth E]
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
HA [auth H]
KA [auth I]
M [auth A]
BA [auth F],
EA [auth G],
HA [auth H],
KA [auth I],
M [auth A],
NA [auth J],
P [auth B],
S [auth C],
V [auth D],
Y [auth E]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.239α = 68.13
b = 100.3β = 85.76
c = 100.786γ = 89.3
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction

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