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Lyase PDB id
1nzy
Jmol
Contents
Protein chains
269 a.a. *
Ligands
BCA ×3
PO4
EDO ×2
Metals
_CA ×3
Waters ×598
* Residue conservation analysis
PDB id:
1nzy
Name: Lyase
Title: 4-chlorobenzoyl coenzyme a dehalogenase from pseudomonas sp. Cbs-3
Structure: 4-chlorobenzoyl coenzyme a dehalogenase. Chain: a, c. Synonym: dehalogenase. Engineered: yes. 4-chlorobenzoyl coenzyme a dehalogenase. Chain: b. Synonym: dehalogenase. Engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 72586. Strain: cbs-3. Expressed in: escherichia coli. Expression_system_taxid: 562. Pseudomonas sp. Cbs3. Expression_system_taxid: 562
Biol. unit: Hexamer (from PQS)
Resolution:
1.80Å     R-factor:   0.188    
Authors: M.M.Benning,H.M.Holden
Key ref:
M.M.Benning et al. (1996). Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: an enzyme catalyst generated via adaptive mutation. Biochemistry, 35, 8103-8109. PubMed id: 8679561 DOI: 10.1021/bi960768p
Date:
02-Apr-96     Release date:   07-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
A5JTM5  (CBADH_PSEUC) -  4-chlorobenzoyl coenzyme A dehalogenase
Seq:
Struc: 		269 a.a.
269 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.8.1.7  - 4-chlorobenzoyl-CoA dehalogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-chlorobenzoyl-CoA + H2O = 4-hydroxybenzoyl CoA + chloride
4-chlorobenzoyl-CoA
 + H(2)O
 =
4-hydroxybenzoyl CoA
Bound ligand (Het Group name = BCA)
matches with 92.98% similarity 		+ chloride
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi960768p Biochemistry 35:8103-8109 (1996)
PubMed id: 8679561  
 
 
Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 A resolution: an enzyme catalyst generated via adaptive mutation.
M.M.Benning, K.L.Taylor, Liu R-Q, G.Yang, H.Xiang, G.Wesenberg, D.Dunaway-Mariano, H.M.Holden.
 
  ABSTRACT  
 
Here we describe the three-dimensional structure of 4-chlorobenzoyl-CoA dehalogenase from Pseudomonas sp. strain CBS-3. This enzyme catalyzes the hydrolysis of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA. The molecular structure of the enzyme/4-hydroxybenzoyl-CoA complex was solved by the techniques of multiple isomorphous replacement, solvent flattening, and molecular averaging. Least-squares refinement of the protein model reduced the crystallographic R factor to 18.8% for all measured X-ray data from 30 to 1.8 A resolution. The crystallographic investigation of this dehalogenase revealed that the enzyme is a trimer. Each subunit of the trimer folds into two distinct motifs. The larger, N-terminal domain is characterized by 10 strands of beta-pleated sheet that form two distinct layers which lie nearly perpendicular to one another. These layers of beta-sheet are flanked on either side by alpha-helices. The C-terminal domain extends away from the body of the molecule and is composed of three amphiphilic alpha-helices. This smaller domain is primarily involved in trimerization. The two domains of the subunit are linked together by a cation, most likely a calcium ion. The 4-hydroxybenzoyl-CoA molecule adopts a curved conformation within the active site such that the 4-hydroxybenzoyl and the adenosine moieties are buried while the pantothenate and pyrophosphate groups of the coenzyme are more solvent exposed. From the three-dimensional structure it is clear that Asp 145 provides the side-chain carboxylate group that adds to form the Meisenheimer intermediate and His 90 serves as the general base in the subsequent hydrolysis step. Many of the structural principles derived from this investigation may be directly applicable to other related enzymes such as crotonase.
 

Literature references that cite this PDB file's key reference

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Delta3,5-delta2,4-dienoyl-CoA isomerase from rat liver. Molecular characterization.
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Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates.
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Non-enzymatic and enzymatic hydrolysis of alkyl halides: a haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction.
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Three-dimensional structure of L-2-haloacid dehalogenase from Xanthobacter autotrophicus GJ10 complexed with the substrate-analogue formate.
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PDB code: 1aq6
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Raman study of the polarizing forces promoting catalysis in 4-chlorobenzoate-CoA dehalogenase.
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Investigation of substrate activation by 4-chlorobenzoyl-coenzyme A dehalogenase.
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.