6NIB

Crystal Structure of Medicago truncatula Agmatine Iminohydrolase (Deiminase)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.112 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Study of Agmatine Iminohydrolase FromMedicago truncatula, the Second Enzyme of the Agmatine Route of Putrescine Biosynthesis in Plants.

Sekula, B.Dauter, Z.

(2019) Front Plant Sci 10: 320-320

  • DOI: https://doi.org/10.3389/fpls.2019.00320
  • Primary Citation of Related Structures:  
    6NIB, 6NIC

  • PubMed Abstract: 

    Plants are unique eukaryotes that can produce putrescine (PUT), a basic diamine, from arginine via a three-step pathway. This process starts with arginine decarboxylase that converts arginine to agmatine. Then, the consecutive action of two hydrolytic enzymes, agmatine iminohydrolase (AIH) and N- carbamoylputrescine amidohydrolase, ultimately produces PUT. An alternative route of PUT biosynthesis requires ornithine decarboxylase that catalyzes direct putrescine biosynthesis. However, some plant species lack this enzyme and rely only on agmatine pathway. The scope of this manuscript concerns the structural characterization of AIH from the model legume plant, Medicago truncatula . Mt AIH is a homodimer built of two subunits with a characteristic propeller fold, where five αββαβ repeated units are arranged around the fivefold pseudosymmetry axis. Dimeric assembly of this plant AIH, formed by interactions of conserved structural elements from one repeat, is drastically different from that observed in dimeric bacterial AIHs. Additionally, the structural snapshot of Mt AIH in complex with 6-aminohexanamide, the reaction product analog, presents the conformation of the enzyme during catalysis. Our structural results show that Mt AIH undergoes significant structural rearrangements of the long loop, which closes a tunnel-shaped active site over the course of the catalytic event. This conformational change is also observed in AIH from Arabidopsis thaliana , indicating the importance of the closed conformation of the gate-keeping loop for the catalysis of plant AIHs.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Porphyromonas-type peptidyl-arginine deiminase367Medicago truncatulaMutation(s): 0 
Gene Names: 11445422MTR_4g112810MtrunA17_Chr4g0061951
EC: 3.5.3.12
UniProt
Find proteins for G7JT50 (Medicago truncatula)
Explore G7JT50 
Go to UniProtKB:  G7JT50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7JT50
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.112 
  • R-Value Observed: 0.112 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.996α = 90
b = 75.504β = 108.56
c = 47.103γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
STARANISOdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description