4FPI

Crystal Structure of 5-chloromuconolactone isomerase from Rhodococcus opacus 1CP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray crystallographic and molecular docking studies on a unique chloromuconolactone dehalogenase from Rhodococcus opacus 1CP.

Ferraroni, M.Kolomytseva, M.Golovleva, L.A.Scozzafava, A.

(2013) J.Struct.Biol. 182: 44-50

  • DOI: 10.1016/j.jsb.2013.01.006

  • PubMed Abstract: 
  • 5-Chloromuconolactone dehalogenase (5-CMLD) is a unique enzyme that catalyzes the conversion of 5-chloromuconolactone into cis-dienelactone in the new modified ortho-pathway of the 3-chlorocatechol degradation by Rhodococcus opacus 1CP. In all other ...

    5-Chloromuconolactone dehalogenase (5-CMLD) is a unique enzyme that catalyzes the conversion of 5-chloromuconolactone into cis-dienelactone in the new modified ortho-pathway of the 3-chlorocatechol degradation by Rhodococcus opacus 1CP. In all other known chlorocatechol pathways the dehalogenation is a spontaneous secondary reaction of the unstable chloromuconate intermediate following the lactonization process catalyzed by the muconate cycloisomerases. The crystallographic structure of the decameric 5-CMLD was solved by Molecular Replacement, using the coordinates of the low resolution structure of the highly homologous muconolactone isomerase, an enzyme of the conventional ortho-pathway. Muconolactone isomerase catalyzes the endocyclic rearrangement of the double bond within the lactone ring of muconolactone to yield 3-oxoadipate enol lactone. Although both 5-CMLD and muconolactone isomerase share the ability to dechlorinate 5-chloromuconolactone, 5-CMLD shows a significant degree of specialization, having lost the capacity to convert its original substrate muconolactone. The active site of 5-CMLD was previously hypothesized to reside in a deep pocket at the interface of two different subunits, on the basis of a muconolactone isomerase structure analysis. In this study we also performed molecular docking calculations that confirmed these previous findings, and allowed us furthermore to determine the residues involved in the catalytic process.


    Organizational Affiliation

    Dipartimento di Chimica Ugo Schiff, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino (FI), Italy. marta.ferraroni@unifi.it




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-chloromuconolactone dehalogenase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U
94Rhodococcus opacusMutation(s): 0 
Gene Names: clcF
EC: 5.3.3.4
Find proteins for Q8G9L0 (Rhodococcus opacus)
Go to UniProtKB:  Q8G9L0
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 122.187α = 90.00
b = 79.657β = 105.54
c = 125.907γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release