Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

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Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily

Ahn, H.J.Kim, K.H.Lee, J.Ha, J.-Y.Lee, H.H.Kim, D.Yoon, H.-J.Kwon, A.-R.Suh, S.W.

(2004) J Biol Chem 279: 50505-50513

  • DOI: https://doi.org/10.1074/jbc.M409246200
  • Primary Citation of Related Structures:  
    1WOG, 1WOH, 1WOI

  • PubMed Abstract: 

    Agmatine is the product of arginine decarboxylation and can be hydrolyzed by agmatinase to putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. Besides being an intermediate in polyamine metabolism, recent findings indicate that agmatine may play important regulatory roles in mammals. Agmatinase is a binuclear manganese metalloenzyme and belongs to the ureohydrolase superfamily that includes arginase, formiminoglutamase, and proclavaminate amidinohydrolase. Compared with a wealth of structural information available for arginases, no three-dimensional structure of agmatinase has been reported. Agmatinase from Deinococcus radiodurans, a 304-residue protein, shows approximately 33% of sequence identity to human mitochondrial agmatinase. Here we report the crystal structure of D. radiodurans agmatinase in Mn(2+)-free, Mn(2+)-bound, and Mn(2+)-inhibitor-bound forms, representing the first structure of agmatinase. It reveals the conservation as well as variation in folding, oligomerization, and the active site of the ureohydrolase superfamily. D. radiodurans agmatinase exists as a compact homohexamer of 32 symmetry. Its binuclear manganese cluster is highly similar but not identical to the clusters of arginase and proclavaminate amidinohydrolase. The structure of the inhibited complex reveals that inhibition by 1,6-diaminohexane arises from the displacement of the metal-bridging water.

  • Organizational Affiliation

    Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

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
305Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RZ04 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RZ04 
Go to UniProtKB:  Q9RZ04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RZ04
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MN

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

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.764α = 90
b = 130.759β = 90
c = 168.746γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations