5MXP | pdb_00005mxp

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 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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 = 65.9 °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: 
    • Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic. lukchrast@gmail.com.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha/beta hydrolase
A, B
302Marinobacter sp. ELB17Mutation(s): 0 
Gene Names: MELB17_23105
EC: 3.8.1.5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
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

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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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary