Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.98 kDa 
• Atom Count: 9233 
• Modelled Residue Count: 932 
• Deposited Residue Count: 940 
• Unique protein chains: 1

3ZNU

Crystal structure of ClcF in crystal form 2

• DOI: 10.2210/pdb3ZNU/pdb

• Classification: LYASE
• Organism(s): Rhodococcus opacus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-18 Released: 2013-02-27 
• Deposition Author(s): Roth, C., Groening, J.A.D., Kaschabek, S.R., Schloemann, M., Straeter, N.

---

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 

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

• PubMed: 23421784 
• 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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-CHLOROMUCONOLACTONE DEHALOGENASE	A, B, C, D, E, F, G, H, I, J	94	Rhodococcus opacus	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	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
CL	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
MG	AA [auth D], NA [auth H], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 78.242	α = 90
b = 103.574	β = 90
c = 141.667	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-18 
• Released Date: 2013-02-27 
Deposition Author(s): Roth, C., Groening, J.A.D., Kaschabek, S.R., Schloemann, M., Straeter, N.

Revision History  

• 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