3RVA

Crystal structure of organophosphorus acid anhydrolase from Alteromonas macleodii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Organophosphorus acid anhydrolase from Alteromonas macleodii: structural study and functional relationship to prolidases.

Stepankova, A.Duskova, J.Skalova, T.Hasek, J.Koval, T.Ostergaard, L.H.Dohnalek, J.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 346-354

  • DOI: 10.1107/S1744309113002674
  • Primary Citation of Related Structures:  
    3RVA

  • PubMed Abstract: 
  • The bacterial enzyme organophosphorus acid anhydrolase (OPAA) is able to catalyze the hydrolysis of both proline dipeptides (Xaa-Pro) and several types of organophosphate (OP) compounds. The full three-dimensional structure of the manganese-dependent OPAA enzyme is presented for the first time ...

    The bacterial enzyme organophosphorus acid anhydrolase (OPAA) is able to catalyze the hydrolysis of both proline dipeptides (Xaa-Pro) and several types of organophosphate (OP) compounds. The full three-dimensional structure of the manganese-dependent OPAA enzyme is presented for the first time. This enzyme, which was originally isolated from the marine bacterium Alteromonas macleodii, was prepared recombinantly in Escherichia coli. The crystal structure was determined at 1.8 Å resolution in space group C2, with unit-cell parameters a = 133.8, b = 49.2, c = 97.3 Å, β = 125.0°. The enzyme forms dimers and their existence in solution was confirmed by dynamic light scattering and size-exclusion chromatography. The enzyme shares the pita-bread fold of its C-terminal domain with related prolidases. The binuclear manganese centre is located in the active site within the pita-bread domain. Moreover, an Ni(2+) ion from purification was localized according to anomalous signal. This study presents the full structure of this enzyme with complete surroundings of the active site and provides a critical analysis of its relationship to prolidases.


    Organizational Affiliation

    Institute of Macromolecular Chemistry, AS CR, vvi, Heyrovsky sq 2, 162 06 Prague 6, Czech Republic. a.stepanko@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Organophosphorus acid anhydrolaseA451Alteromonas macleodiiMutation(s): 0 
Gene Names: pepQBFV94_0545TE101_02590
EC: 3.1.8.2 (PDB Primary Data), 3.4.13.9 (PDB Primary Data)
UniProt
Find proteins for F8UVJ4 (Alteromonas macleodii)
Explore F8UVJ4 
Go to UniProtKB:  F8UVJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8UVJ4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.77α = 90
b = 49.19β = 125.03
c = 97.34γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Database references