7LOL

The structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity.

Maturana, P.Orellana, M.S.Herrera, S.M.Martinez, I.Figueroa, M.Martinez-Oyanedel, J.Castro-Fernandez, V.Uribe, E.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms22094769
  • Primary Citation of Related Structures:  
    7LOL, 7LOX

  • PubMed Abstract: 

    Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer's, Parkinson's, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from Escherichia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 Å), including a guanidine group; and other at high resolution (1.8 Å) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn 2+ and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.


  • Organizational Affiliation

    Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Ñuñoa 7800003, Santiago, Chile.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Agmatinase306Escherichia coliMutation(s): 0 
Gene Names: speB
EC: 3.5.3.11
UniProt
Find proteins for P60651 (Escherichia coli (strain K12))
Explore P60651 
Go to UniProtKB:  P60651
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60651
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AG2 (Subject of Investigation/LOI)
Query on AG2

Download Ideal Coordinates CCD File 
B [auth A]AGMATINE
C5 H14 N4
QYPPJABKJHAVHS-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
URE (Subject of Investigation/LOI)
Query on URE

Download Ideal Coordinates CCD File 
F [auth A]UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.746α = 90
b = 81.746β = 90
c = 207.436γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
BALBESphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Comision Nacional Cientifica y Technologica (CONICYT)ChileFONDECYT 11181133
Comision Nacional Cientifica y Technologica (CONICYT)ChileREDI170497
Comision Nacional Cientifica y Technologica (CONICYT)ChileFondequip EQM140151

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description