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Hydrolase PDB id
1g5f
Jmol
Contents
Protein chain
294 a.a. *
Ligands
DCE
Metals
_CA ×3
_CL
Waters ×275
* Residue conservation analysis
PDB id:
1g5f
Name: Hydrolase
Title: Structure of linb complexed with 1,2-dichloroethane
Structure: 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase. Chain: a. Synonym: 1,4-tcdn chlorohydrolase. Engineered: yes
Source: Sphingomonas paucimobilis. Organism_taxid: 13689. Gene: linb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.80Å     R-factor:   0.173     R-free:   0.198
Authors: A.J.Oakley,Z.Prokop,M.Bohac,J.Kmunicek,T.Jedlicka, M.Monincova,I.Kuta-Smatanova,Y.Nagata,J.Damborsky, M.C.J.Wilce
Key ref:
A.J.Oakley et al. (2002). Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition. Biochemistry, 41, 4847-4855. PubMed id: 11939779 DOI: 10.1021/bi015734i
Date:
01-Nov-00     Release date:   01-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P51698  (LINB_PSEPA) -  Haloalkane dehalogenase
Seq:
Struc: 		296 a.a.
294 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.8.1.5  - Haloalkane dehalogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 1-haloalkane + H2O = a primary alcohol + halide
1-haloalkane
 + H(2)O
 = primary alcohol
 + halide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     response to toxin   1 term 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi015734i Biochemistry 41:4847-4855 (2002)
PubMed id: 11939779  
 
 
Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.
A.J.Oakley, Z.Prokop, M.Bohác, J.Kmunícek, T.Jedlicka, M.Monincová, I.Kutá-Smatanová, Y.Nagata, J.Damborský, M.C.Wilce.
 
  ABSTRACT  
 
The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases. The study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste. We report the kinetic and structural analysis of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) in complex with each of 1,2-dichloroethane and 1,2-dichloropropane and the reaction product of 1-chlorobutane turnover. Activity studies showed very weak but detectable activity of LinB with 1,2-dichloroethane [0.012 nmol s(-1) (mg of enzyme)(-1)] and 1,2-dichloropropane [0.027 nmol s(-1) (mg of enzyme)(-1)]. These activities are much weaker compared, for example, to the activity of LinB with 1-chlorobutane [68.2 nmol s(-1) (mg of enzyme)(-1)]. Inhibition analysis reveals that both 1,2-dichloroethane and 1,2-dichloropropane act as simple competitive inhibitors of the substrate 1-chlorobutane and that 1,2-dichloroethane binds to LinB with lower affinity than 1,2-dichloropropane. Docking calculations on the enzyme in the absence of active site water molecules and halide ions confirm that these compounds could bind productively. However, when these moieties were included in the calculations, they bound in a manner similar to that observed in the crystal structure. These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20197499 R.Lal, G.Pandey, P.Sharma, K.Kumari, S.Malhotra, R.Pandey, V.Raina, H.P.Kohler, C.Holliger, C.Jackson, and J.G.Oakeshott (2010).
Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation.
  Microbiol Mol Biol Rev, 74, 58-80.  
17259360 M.Monincová, Z.Prokop, J.Vévodová, Y.Nagata, and J.Damborsky (2007).
Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry.
  Appl Environ Microbiol, 73, 2005-2008.
PDB code: 2bfn
17634937 Y.Nagata, R.Endo, M.Ito, Y.Ohtsubo, and M.Tsuda (2007).
Aerobic degradation of lindane (gamma-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis.
  Appl Microbiol Biotechnol, 76, 741-752.  
16792811 M.Petrek, M.Otyepka, P.Banás, P.Kosinová, J.Koca, and J.Damborský (2006).
CAVER: a new tool to explore routes from protein clefts, pockets and cavities.
  BMC Bioinformatics, 7, 316.  
17016745 P.Banás, M.Otyepka, P.Jerábek, M.Petrek, and J.Damborský (2006).
Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.
  J Comput Aided Mol Des, 20, 375-383.  
15062775 D.B.Janssen (2004).
Evolving haloalkane dehalogenases.
  Curr Opin Chem Biol, 8, 150-159.  
14525993 R.Chaloupková, J.Sýkorová, Z.Prokop, A.Jesenská, M.Monincová, M.Pavlová, M.Tsuda, Y.Nagata, and J.Damborský (2003).
Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel.
  J Biol Chem, 278, 52622-52628.  
14675551 R.M.de Jong, and B.W.Dijkstra (2003).
Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond.
  Curr Opin Struct Biol, 13, 722-730.  
12939138 V.A.Streltsov, Z.Prokop, J.Damborský, Y.Nagata, A.Oakley, and M.C.Wilce (2003).
Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates.
  Biochemistry, 42, 10104-10112.
PDB codes: 1iz7 1iz8 1k5p 1k63 1k6e
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.