Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 39.64 kDa 
• Atom Count: 3016 
• Modelled Residue Count: 369 
• Deposited Residue Count: 370 
• Unique protein chains: 1

1NU5

Crystal structure of Pseudomonas sp. P51 Chloromuconate lactonizing enzyme

• PDB DOI: 10.2210/pdb1NU5/pdb

• Classification: ISOMERASE
• Organism(s): Pseudomonas sp. P51
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-01-31 Released: 2003-12-30 
• Deposition Author(s): Kajander, T., Lehtio, L., Goldman, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.231 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.

Kajander, T., Lehtio, L., Schlomann, M., Goldman, A.

(2003) Protein Sci 12: 1855-1864

• PubMed: 12930985 
• DOI: 10.1110/ps.0388503
• Primary Citation of Related Structures:  
  1NU5


• PubMed Abstract: 
  

Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis-muconate as a part of the beta-ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl-MLEs). The basis for the Cl-MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl-MLEs, we have solved the structure of Pseudomonas P51 Cl-MLE at 1.95 A resolution. Comparison of Pseudomonas MLE and Cl-MLE structures reveals the presence of a large cavity in the Cl-MLEs. The cavity may be related to conformational changes on substrate binding in Cl-MLEs, at Gly52. Site-directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl-MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly-Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl-MLEs. The Cl-MLE structure, as a result of the Thr-to-Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl-MLEs. The loose packing and structural motions in Cl-MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl-MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl-MLEs result in lower active site polarity in Cl-MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl-MLEs and make it a better enzyme for dehalogenation of substrate.

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Organizational Affiliation: 

Research Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloromuconate cycloisomerase	A	370	Pseudomonas sp. P51	Mutation(s): 0  Gene Names: tcbD EC: 5.5.1.7
UniProt
Find proteins for P27099 (Pseudomonas sp. (strain P51)) Explore P27099  Go to UniProtKB:  P27099

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.231 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.355	α = 90
b = 135.355	β = 90
c = 105.033	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-31 
• Released Date: 2003-12-30 
Deposition Author(s): Kajander, T., Lehtio, L., Goldman, A.

Revision History  

• Version 1.0: 2003-12-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2018-05-23
  Changes: Data collection