3ZNU

Crystal structure of ClcF in crystal form 2

PDB DOI: https://doi.org/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

wwPDB Validation 3D Report Full Report

This is version 1.4 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

PubMed: 23421784 Search on PubMed
DOI: https://doi.org/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.

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.

Macromolecule Content

Total Structure Weight: 113.98 kDa
Atom Count: 9,233
Modelled Residue Count: 932
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-CHLOROMUCONOLACTONE DEHALOGENASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	94	Rhodococcus opacus	Mutation(s): 0
UniProt
Find proteins for Q8G9L0 (Rhodococcus opacus) Explore Q8G9L0 Go to UniProtKB: Q8G9L0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8G9L0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain OA [auth H] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain Q [auth B] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain UA [auth J] SDF format, chain VA [auth J] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth J] MOL2 format, chain VA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	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		Interactions Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth J] Focus chain VA [auth J] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain KA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth J] Focus chain VA [auth J] Focus chain Y [auth D] Focus chain Z [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain K [auth A] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain QA [auth I] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain TA [auth J] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain TA [auth J] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D]	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		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain QA [auth I] Focus chain R [auth C] Focus chain S [auth C] Focus chain TA [auth J] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain K [auth A] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth B] Focus chain O [auth B] Focus chain QA [auth I] Focus chain R [auth C] Focus chain S [auth C] Focus chain TA [auth J] Focus chain V [auth D] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain NA [auth H] SDF format, chain X [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain NA [auth H] MOL2 format, chain X [auth D]	AA [auth D], NA [auth H], X [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain NA [auth H] Focus chain X [auth D] Interactions & Density Focus chain AA [auth D] Focus chain NA [auth H] Focus chain X [auth D]

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-02-27

Deposition Author(s):

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
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description