E. coli Agmatinase

  • Classification: HYDROLASE
  • Organism(s): Escherichia coli
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-01-07 Released: 2021-03-31 
  • Deposition Author(s): Chitrakar, I., Ahmed, S.F., Torelli, A.T., French, J.B.
  • Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structure of the E. coli agmatinase, SPEB.

Chitrakar, I.Ahmed, S.F.Torelli, A.T.French, J.B.

(2021) PLoS One 16: e0248991-e0248991

  • DOI: https://doi.org/10.1371/journal.pone.0248991
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E. coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P31 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/Rfree values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.

  • Organizational Affiliation

    Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, United States of America.

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, M, N, O, P, Q, R
329Escherichia coliMutation(s): 0 
Gene Names: speBWG5_03731
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MN

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

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.809α = 90
b = 139.809β = 90
c = 222.987γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1750637
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103403
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10RR029205

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description