PDBsum entry 1wog

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
(+ 0 more) 303 a.a. *
16D ×6
_MN ×12
Waters ×843
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily
Structure: Agmatinase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Deinococcus radiodurans. Organism_taxid: 1299. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
1.80Å     R-factor:   0.223     R-free:   0.251
Authors: H.J.Ahn,K.H.Kim,J.Lee,J.-Y.Ha,H.H.Lee,D.Kim,H.-J.Yoon,A.- R.Kwon,S.W.Suh
Key ref:
H.J.Ahn et al. (2004). Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily. J Biol Chem, 279, 50505-50513. PubMed id: 15355972 DOI: 10.1074/jbc.M409246200
18-Aug-04     Release date:   07-Sep-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9RZ04  (Q9RZ04_DEIRA) -  Agmatinase, putative
304 a.a.
303 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  


DOI no: 10.1074/jbc.M409246200 J Biol Chem 279:50505-50513 (2004)
PubMed id: 15355972  
Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily.
H.J.Ahn, K.H.Kim, J.Lee, J.Y.Ha, H.H.Lee, D.Kim, H.J.Yoon, A.R.Kwon, S.W.Suh.
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.
  Selected figure(s)  
Figure 1.
FIG. 1. Metabolism of L-arginine and substrates of ureohydrolase superfamily. A, two metabolic pathways of L-arginine to purtrescine. B, various types of substrate for the ureohydrolase superfamily enzymes. i, agmatine. ii, arginine. iii, formiminoglutamate. iv, guanidinoproclavaminic acid. ODC, ornithine decarboxylase; ADC, arginine decarboxylase.
Figure 6.
FIG. 6. Homology modeled structure of human mitochondrial agmatinase. A, stereodiagram of C superposition of DR agmatinase structure (gray) and the human agmatinase model (orange), which was built by homology modeling (SWISS-MODEL server). The amino and carboxyl termini of DR agmatinase are indicated by N' and C', respectively, whereas those of human agmatinase are indicated by Ser67 and Thr351, respectively. B, active sites of DR agmatinase and human agmatinase are superimposed. The orientation of the figure and atom coloring are the same as in Fig. 5A, except the carbon atoms of DR and human are in gray and orange, respectively. Residues names and numbering of DR agmatinase follow those of human agmatinase.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 50505-50513) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20607275 C.Mella, F.Martínez, Los Angeles García, F.Nualart, V.Castro, P.Bustos, N.Carvajal, and E.Uribe (2010).
Expression and localization of an agmatinase-like protein in the rat brain.
  Histochem Cell Biol, 134, 137-144.  
19093830 E.Y.Shishova, L.Di Costanzo, F.A.Emig, D.E.Ash, and D.W.Christianson (2009).
Probing the specificity determinants of amino acid recognition by arginase.
  Biochemistry, 48, 121-131.
PDB codes: 3e6k 3e6v 3e8q 3e8z 3e9b
19456858 G.A.Wells, I.B.Müller, C.Wrenger, and A.I.Louw (2009).
The activity of Plasmodium falciparum arginase is mediated by a novel inter-monomer salt-bridge between Glu295-Arg404.
  FEBS J, 276, 3517-3530.  
18331637 K.Manikandan, D.Pal, S.Ramakumar, N.E.Brener, S.S.Iyengar, and G.Seetharaman (2008).
Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments.
  Genome Biol, 9, R52.  
17212779 R.Alarcón, M.S.Orellana, B.Neira, E.Uribe, J.R.García, and N.Carvajal (2006).
Mutational analysis of substrate recognition by human arginase type I--agmatinase activity of the N130D variant.
  FEBS J, 273, 5625-5631.  
16128822 V.López, R.Alarcón, M.S.Orellana, P.Enríquez, E.Uribe, J.Martínez, and N.Carvajal (2005).
Insights into the interaction of human arginase II with substrate and manganese ions by site-directed mutagenesis and kinetic studies. Alteration of substrate specificity by replacement of Asn149 with Asp.
  FEBS J, 272, 4540-4548.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.