Arginase from Medicago truncatula in complex with ornithine

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

Starting Model: experimental
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The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.

Sekula, B.

(2020) Front Plant Sci 11: 987-987

  • DOI: https://doi.org/10.3389/fpls.2020.00987
  • Primary Citation of Related Structures:  
    6VSS, 6VST, 6VSU

  • PubMed Abstract: 

    Arginine acts as a precursor of polyamines in plants in two known pathways, agmatine and ornithine routes. It is decarboxylated to agmatine by arginine decarboxylase, and then transformed to putrescine by the consecutive action of agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase. Alternatively, it can be hydrolyzed to ornithine by arginase and then decarboxylated by ornithine decarboxylase to putrescine. Some plants lack a functional ornithine pathway, but all have one or two arginases that can have dual cellular localization, in mitochondria and plastids. It was recently shown that arginases from Arabidopsis thaliana and soybean act also as agmatinases, thus they can produce putrescine directly from agmatine. Therefore, arginase (together with arginine decarboxylase) can complement putrescine production in plastids, providing a third polyamine biosynthesis pathway in plants. Phylogenetic analysis suggests that arginases, highly conserved in the plant kingdom, create the only group of enzymes recognized in the family of ureohydrolases in plants. Arginases are metalloenzymes with binuclear manganese cluster in the active site. In this work, two arginases from A. thaliana and Medicago truncatula are structurally characterized and their binding properties are discussed. Crystal structures with bound ornithine show that plant hexameric arginases engage a long loop from the neighboring subunit to stabilize α-amino and carboxyl groups of the ligand. This unique ligand binding mode is unobserved in arginases from other domains of life. Structural analysis shows that substrate binding by residues from two neighboring subunits might also characterize some prokaryotic agmatinases. This feature of plant arginases is most likely the determinant of their ability to recognize not only arginine but also agmatine as their substrates, thus, to act as arginase and agmatinase.

  • Organizational Affiliation

    Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
341Medicago truncatulaMutation(s): 0 
Gene Names: 11420737MTR_4g024960MtrunA17_Chr4g0011501
Find proteins for G7JFU5 (Medicago truncatula)
Explore G7JFU5 
Go to UniProtKB:  G7JFU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7JFU5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ORN (Subject of Investigation/LOI)
Query on ORN

Download Ideal Coordinates CCD File 
BA [auth F]
GA [auth H]
LA [auth J]
O [auth A]
QA [auth L]
BA [auth F],
GA [auth H],
LA [auth J],
O [auth A],
QA [auth L],
R [auth B],
W [auth D]
C5 H12 N2 O2
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
DA [auth G]
EA [auth H]
FA [auth H]
AA [auth F],
CA [auth G],
DA [auth G],
EA [auth H],
FA [auth H],
HA [auth I],
IA [auth I],
JA [auth J],
KA [auth J],
M [auth A],
MA [auth K],
N [auth A],
NA [auth K],
OA [auth L],
P [auth B],
PA [auth L],
Q [auth B],
S [auth C],
T [auth C],
U [auth D],
V [auth D],
X [auth E],
Y [auth E],
Z [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.672α = 90
b = 166.074β = 94.5
c = 150.875γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2020-08-12 
  • Deposition Author(s): Sekula, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description