5MXP

Haloalkane dehalogenase DmxA from Marinobacter sp. ELB17 possessing a unique catalytic residue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic BacteriumMarinobactersp. ELB17.

Chrast, L.Tratsiak, K.Planas-Iglesias, J.Daniel, L.Prudnikova, T.Brezovsky, J.Bednar, D.Kuta Smatanova, I.Chaloupkova, R.Damborsky, J.

(2019) Microorganisms 7

  • DOI: 10.3390/microorganisms7110498
  • Primary Citation of Related Structures:  
    5MXP

  • PubMed Abstract: 
  • Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature T m,app = 65 ...

    Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature T m,app = 65.9 °C) of all biochemically characterized wild type haloalkane dehalogenases belonging to subfamily II. The enzyme was successfully expressed and its crystal structure was solved at 1.45 Å resolution. DmxA structure contains several features distinct from known members of haloalkane dehalogenase family: (i) a unique composition of catalytic residues; (ii) a dimeric state mediated by a disulfide bridge; and (iii) narrow tunnels connecting the enzyme active site with the surrounding solvent. The importance of narrow tunnels in such paradoxically high stability of DmxA enzyme was confirmed by computational protein design and mutagenesis experiments.


    Organizational Affiliation

    International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic. jiri@chemi.muni.cz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha/beta hydrolaseA, B302Marinobacter sp. ELB17Mutation(s): 0 
Gene Names: MELB17_23105
EC: 3.8.1.5
UniProt
Find proteins for A3JB27 (Marinobacter sp. ELB17)
Explore A3JB27 
Go to UniProtKB:  A3JB27
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3JB27
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.371α = 90
b = 78.343β = 90
c = 150.514γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant AgencyCzech RepublicP207/12/0775
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: 2018-07-25
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references