6F9O

Crystal structure of cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.111 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5.

Tratsiak, K.Prudnikova, T.Drienovska, I.Damborsky, J.Brynda, J.Pachl, P.Kuty, M.Chaloupkova, R.Rezacova, P.Kuta Smatanova, I.

(2019) Acta Crystallogr F Struct Biol Commun 75: 324-331

  • DOI: 10.1107/S2053230X19002796
  • Primary Citation of Related Structures:  
    6F9O

  • PubMed Abstract: 
  • Haloalkane dehalogenases (HLDs) convert halogenated aliphatic pollutants to less toxic compounds by a hydrolytic mechanism. Owing to their broad substrate specificity and high enantioselectivity, haloalkane dehalogenases can function as biosensors to detect toxic compounds in the environment or can be used for the production of optically pure compounds ...

    Haloalkane dehalogenases (HLDs) convert halogenated aliphatic pollutants to less toxic compounds by a hydrolytic mechanism. Owing to their broad substrate specificity and high enantioselectivity, haloalkane dehalogenases can function as biosensors to detect toxic compounds in the environment or can be used for the production of optically pure compounds. Here, the structural analysis of the haloalkane dehalogenase DpcA isolated from the psychrophilic bacterium Psychrobacter cryohalolentis K5 is presented at the atomic resolution of 1.05 Å. This enzyme exhibits a low temperature optimum, making it attractive for environmental applications such as biosensing at the subsurface environment, where the temperature typically does not exceed 25°C. The structure revealed that DpcA possesses the shortest access tunnel and one of the most widely open main tunnels among structural homologs of the HLD-I subfamily. Comparative analysis revealed major differences in the region of the α4 helix of the cap domain, which is one of the key determinants of the anatomy of the tunnels. The crystal structure of DpcA will contribute to better understanding of the structure-function relationships of cold-adapted enzymes.


    Related Citations: 
    • Crystallographic analysis of new psychrophilic haloalkane dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17.
      Tratsiak, K., Degtjarik, O., Drienovska, I., Chrast, L., Rezacova, P., Kuty, M., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.
      (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 683
    • Biochemical characterization of a novel haloalkane dehalogenase from a cold-adapted bacterium.
      Drienovska, I., Chovancova, E., Koudelakova, T., Damborsky, J., Chaloupkova, R.
      (2012) Appl Environ Microbiol 78: 4995

    Organizational Affiliation

    Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Haloalkane dehalogenaseA309Psychrobacter cryohalolentis K5Mutation(s): 0 
Gene Names: dhmAPcryo_1253
EC: 3.8.1.5
UniProt
Find proteins for Q1QBB9 (Psychrobacter cryohalolentis (strain ATCC BAA-1226 / DSM 17306 / VKM B-2378 / K5))
Explore Q1QBB9 
Go to UniProtKB:  Q1QBB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1QBB9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.332α = 90
b = 79.451β = 94.98
c = 43.489γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant AgencyCzech RepublicGACR 17-24321S/P305
Grant AgencyCzech RepublicGA16-24223S
Grant AgencyCzech RepublicGA16-06096S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLO1214
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLO1304
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLQ1605
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015051
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015047
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015055

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references