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PDBsum entry 1cv2

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protein links
Hydrolase PDB id
1cv2
Jmol
Contents
Protein chain
293 a.a. *
Waters ×449
* Residue conservation analysis
PDB id:
1cv2
Name: Hydrolase
Title: Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis ut26 at 1.6 a resolution
Structure: Haloalkane dehalogenase. Chain: a. Synonym: linb, 1,3,4,6-tetrachloro-1,4-cyclohexadiene hydrolase. Engineered: yes
Source: Sphingomonas paucimobilis. Organism_taxid: 13689. Strain: ut26. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.58Å     R-factor:   0.152     R-free:   0.211
Authors: J.Marek,J.Vevodova,J.Damborsky,I.Smatanova,L.A.Svensson, J.Newman,Y.Nagata,M.Takagi
Key ref:
J.Marek et al. (2000). Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry, 39, 14082-14086. PubMed id: 11087355 DOI: 10.1021/bi001539c
Date:
22-Aug-99     Release date:   11-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P51698  (LINB_PSEPA) -  Haloalkane dehalogenase
Seq:
Struc:
296 a.a.
293 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     metabolic process   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi001539c Biochemistry 39:14082-14086 (2000)
PubMed id: 11087355  
 
 
Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.
J.Marek, J.Vévodová, I.K.Smatanová, Y.Nagata, L.A.Svensson, J.Newman, M.Takagi, J.Damborský.
 
  ABSTRACT  
 
The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082075 D.R.Brittain, R.Pandey, K.Kumari, P.Sharma, G.Pandey, R.Lal, M.L.Coote, J.G.Oakeshott, and C.J.Jackson (2011).
Competing S(N)2 and E2 reaction pathways for hexachlorocyclohexane degradation in the gas phase, solution and enzymes.
  Chem Commun (Camb), 47, 976-978.  
21307570 T.Kurihara (2011).
A mechanistic analysis of enzymatic degradation of organohalogen compounds.
  Biosci Biotechnol Biochem, 75, 189-198.  
20363940 G.Wang, R.Li, S.Li, and J.Jiang (2010).
A novel hydrolytic dehalogenase for the chlorinated aromatic compound chlorothalonil.
  J Bacteriol, 192, 2737-2745.  
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.  
19218394 K.Jitsumori, R.Omi, T.Kurihara, A.Kurata, H.Mihara, I.Miyahara, K.Hirotsu, and N.Esaki (2009).
X-Ray crystallographic and mutational studies of fluoroacetate dehalogenase from Burkholderia sp. strain FA1.
  J Bacteriol, 191, 2630-2637.  
19701186 M.Pavlova, M.Klvana, Z.Prokop, R.Chaloupkova, P.Banas, M.Otyepka, R.C.Wade, M.Tsuda, Y.Nagata, and J.Damborsky (2009).
Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate.
  Nat Chem Biol, 5, 727-733.  
19551770 T.Kamachi, T.Nakayama, O.Shitamichi, K.Jitsumori, T.Kurihara, N.Esaki, and K.Yoshizawa (2009).
The catalytic mechanism of fluoroacetate dehalogenase: a computational exploration of biological dehalogenation.
  Chemistry, 15, 7394-7403.  
  19342778 T.Prudnikova, T.Mozga, P.Rezacova, R.Chaloupkova, Y.Sato, Y.Nagata, J.Brynda, M.Kuty, J.Damborsky, and I.K.Smatanova (2009).
Crystallization and preliminary X-ray analysis of a novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 353-356.  
18359861 J.Woo, M.H.Howell, and A.G.von Arnim (2008).
Structure-function studies on the active site of the coelenterazine-dependent luciferase from Renilla.
  Protein Sci, 17, 725-735.  
17729274 M.Otyepka, P.Banás, A.Magistrato, P.Carloni, and J.Damborský (2008).
Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods.
  Proteins, 70, 707-717.  
17295320 E.Chovancová, J.Kosinski, J.M.Bujnicki, and J.Damborský (2007).
Phylogenetic analysis of haloalkane dehalogenases.
  Proteins, 67, 305-316.  
17183511 J.Damborský, M.Petrek, P.Banás, and M.Otyepka (2007).
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.
  Biotechnol J, 2, 62-67.  
17516046 M.Ito, Z.Prokop, M.Klvana, Y.Otsubo, M.Tsuda, J.Damborský, and Y.Nagata (2007).
Degradation of beta-hexachlorocyclohexane by haloalkane dehalogenase LinB from gamma-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205.
  Arch Microbiol, 188, 313-325.  
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.  
  17401198 Y.Sato, R.Natsume, M.Tsuda, J.Damborsky, Y.Nagata, and T.Senda (2007).
Crystallization and preliminary crystallographic analysis of a haloalkane dehalogenase, DbjA, from Bradyrhizobium japonicum USDA110.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 294-296.  
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.  
16957186 P.Sharma, V.Raina, R.Kumari, S.Malhotra, C.Dogra, H.Kumari, H.P.Kohler, H.R.Buser, C.Holliger, and R.Lal (2006).
Haloalkane dehalogenase LinB is responsible for beta- and delta-hexachlorocyclohexane transformation in Sphingobium indicum B90A.
  Appl Environ Microbiol, 72, 5720-5727.  
17136732 Z.Prokop, F.Oplustil, J.DeFrank, and J.Damborský (2006).
Enzymes fight chemical weapons.
  Biotechnol J, 1, 1370-1380.  
16269704 A.Jesenská, M.Pavlová, M.Strouhal, R.Chaloupková, I.Tesínská, M.Monincová, Z.Prokop, M.Bartos, I.Pavlík, I.Rychlík, P.Möbius, Y.Nagata, and J.Damborsky (2005).
Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases.
  Appl Environ Microbiol, 71, 6736-6745.  
16187153 U.Frerichs-Deeken, and S.Fetzner (2005).
Dioxygenases without requirement for cofactors: identification of amino acid residues involved in substrate binding and catalysis, and testing for rate-limiting steps in the reaction of 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase.
  Curr Microbiol, 51, 344-352.  
16085827 Y.Sato, M.Monincová, R.Chaloupková, Z.Prokop, Y.Ohtsubo, K.Minamisawa, M.Tsuda, J.Damborsky, and Y.Nagata (2005).
Two rhizobial strains, Mesorhizobium loti MAFF303099 and Bradyrhizobium japonicum USDA110, encode haloalkane dehalogenases with novel structures and substrate specificities.
  Appl Environ Microbiol, 71, 4372-4379.  
15062775 D.B.Janssen (2004).
Evolving haloalkane dehalogenases.
  Curr Opin Chem Biol, 8, 150-159.  
15572767 T.C.Terwilliger (2004).
Using prime-and-switch phasing to reduce model bias in molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 60, 2144-2149.  
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.  
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
12676719 Y.Nagata, Z.Prokop, S.Marvanová, J.Sýkorová, M.Monincová, M.Tsuda, and J.Damborský (2003).
Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB.
  Appl Environ Microbiol, 69, 2349-2355.  
12952988 Z.Prokop, M.Monincová, R.Chaloupková, M.Klvana, Y.Nagata, D.B.Janssen, and J.Damborský (2003).
Catalytic mechanism of the maloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26.
  J Biol Chem, 278, 45094-45100.  
11939779 A.J.Oakley, Z.Prokop, M.Bohác, J.Kmunícek, T.Jedlicka, M.Monincová, I.Kutá-Smatanová, Y.Nagata, J.Damborský, and M.C.Wilce (2002).
Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.
  Biochemistry, 41, 4847-4855.
PDB codes: 1g42 1g4h 1g5f
12147465 A.Jesenská, M.Bartos, V.Czerneková, I.Rychlík, I.Pavlík, and J.Damborský (2002).
Cloning and expression of the haloalkane dehalogenase gene dhmA from Mycobacterium avium N85 and preliminary characterization of DhmA.
  Appl Environ Microbiol, 68, 3724-3730.  
11967377 M.Otyepka, and J.Damborský (2002).
Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains.
  Protein Sci, 11, 1206-1217.  
12089046 T.Bosma, J.Damborský, G.Stucki, and D.B.Janssen (2002).
Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene.
  Appl Environ Microbiol, 68, 3582-3587.  
11404103 D.B.Janssen, J.E.Oppentocht, and G.J.Poelarends (2001).
Microbial dehalogenation.
  Curr Opin Biotechnol, 12, 254-258.  
11764149 J.Damborský, E.Rorije, A.Jesenská, Y.Nagata, G.Klopman, and W.J.Peijnenburg (2001).
Structure-specificity relationships for haloalkane dehalogenases.
  Environ Toxicol Chem, 20, 2681-2689.  
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.