3ZNU

Crystal structure of ClcF in crystal form 2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure and Catalytic Mechanism of Chloromuconolactone Dehalogenase Clcf from Rhodococcus Opacus 1Cp.

Roth, C., Janosch, A.D., Kaschabek, S.R., Schloemann, M., Straeter, N.

(2013) Mol Microbiol 88: 254

  • DOI: 10.1111/mmi.12182
  • Primary Citation of Related Structures:  
    3ZNJ, 3ZNU, 3ZO7

  • PubMed Abstract: 

    • The actinobacterium Rhodococcus opacus 1CP possesses a so far unique variant of the modified 3-oxoadipate pathway for 3-chlorocatechol degradation. One important feature is the novel dehalogenase ClcF, which converts (4R,5S)-5-chloromuconolactone to E-dienelactone ...

    The actinobacterium Rhodococcus opacus 1CP possesses a so far unique variant of the modified 3-oxoadipate pathway for 3-chlorocatechol degradation. One important feature is the novel dehalogenase ClcF, which converts (4R,5S)-5-chloromuconolactone to E-dienelactone. ClcF is related to muconolactone isomerase (MLI, EC 5.3.3.4). The enzyme has a ferredoxin-type fold and forms a homodecamer of 52-symmetry, typical for the MLI family. The active site is formed by residues from two monomers. The complex structure of an E27A variant with bound substrate in conjunction with mutational studies indicate that E27 acts as the proton acceptor in a univalent single-base syn-dehydrohalogenation mechanism. Despite the evolutionary specialization of ClcF, the conserved active-site structures suggest that the proposed mechanism is representative for the MLI family. Furthermore, ClcF represents a novel type of dehalogenase based on an isomerase scaffold.

    Related Citations: 
    • Crystallization and Preliminary Characterization of Chloromuconolactone Dehalogenase from Rhodococcus Opacus 1Cp.
      Roth, C., Kaschabek, S.R., Groning, J.A.D., Handrek, T., Schlomann, M., Strater, N.
      (2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 591
    Organizational Affiliation: 

    Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5-CHLOROMUCONOLACTONE DEHALOGENASE
A, B, C, D, E, F, G, H, I, J
A, B, C, D, E, F, G, H, I, J
94Rhodococcus opacusMutation(s): 0 
Gene Names: clcF, R1CP_39625
EC: 5.3.3.4
UniProt
Find proteins for Q8G9L0 (Rhodococcus opacus)
Explore Q8G9L0 
Go to UniProtKB:  Q8G9L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G9L0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
BA [auth D],
DA [auth E],
EA [auth E],
GA [auth F],
HA [auth F],
BA [auth D],
DA [auth E],
EA [auth E],
GA [auth F],
HA [auth F],
JA [auth G],
KA [auth G],
L [auth A],
M [auth A],
OA [auth H],
P [auth B],
PA [auth H],
Q [auth B],
RA [auth I],
SA [auth I],
T [auth C],
U [auth C],
UA [auth J],
VA [auth J],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
CA [auth E],
FA [auth F],
IA [auth G],
K [auth A],
LA [auth H],
CA [auth E],
FA [auth F],
IA [auth G],
K [auth A],
LA [auth H],
MA [auth H],
N [auth B],
O [auth B],
QA [auth I],
R [auth C],
S [auth C],
TA [auth J],
V [auth D],
W [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth D],
NA [auth H],
X [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.242α = 90
b = 103.574β = 90
c = 141.667γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2013-03-20
    Changes: Atomic model, Other
  • Version 1.3: 2013-04-24
    Changes: Database references