3EJ7 | pdb_00003ej7

Experimental Data Snapshot

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

(2008) Acta Crystallogr D Biol Crystallogr 64: 1277-1282

PubMed Abstract:
Trans-3-chloroacrylic acid dehalogenase (CaaD) is a critical enzyme in the trans-1,3-dichloropropene (DCP) degradation pathway in Pseudomonas pavonaceae 170. This enzyme allows bacteria to use trans-DCP, a common component in commercially produced fumigants, as a carbon source. CaaD specifically catalyzes the fourth step of the pathway by cofactor-independent dehalogenation of a vinyl carbon-halogen bond. Previous studies have reported an X-ray structure of CaaD under acidic conditions with a covalent modification of the catalytic betaPro1 residue. Here, the 1.7 A resolution X-ray structure of CaaD under neutral (pH 6.5) conditions is reported without the presence of the covalent adduct. In this new structure, a substrate-like acetate molecule is bound within the active site in a position analogous to the putative substrate-binding site. Additionally, a catalytically important water molecule was identified, consistent with previously proposed reaction schemes. Finally, flexibility of the catalytically relevant side chain alphaGlu52 is observed in the structure, supporting its role in the catalytic mechanism.

Organizational Affiliation

Center of Pharmaceutical Biotechnology and Department of Medicinal Chemistry and Pharmacognosy, University of Illinois, Chicago, USA. pegan@uic.edu

Macromolecule Content

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-subunit of trans-3-chloroacrylic acid dehalogenase	A, C, E, G, I A, C, E, G, I, K	76	Pseudomonas pavonaceae	Mutation(s): 1 Gene Names: caaD1 EC: 5.3.2.6
UniProt
Find proteins for Q9EV85 (Pseudomonas pavonaceae) Explore Q9EV85 Go to UniProtKB: Q9EV85
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EV85
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-subunit of trans-3-chloroacrylic acid dehalogenase	B, D, F, H, J B, D, F, H, J, L	70	Pseudomonas pavonaceae	Mutation(s): 0 Gene Names: caaD2 EC: 5.3.2.6
UniProt
Find proteins for Q9EV84 (Pseudomonas pavonaceae) Explore Q9EV84 Go to UniProtKB: Q9EV84
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EV84
Sequence Annotations Expand
Reference Sequence

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]