8K40

mercuric reductase,GbsMerA, - FAD bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Biochemical and structural basis of mercuric reductase, GbsMerA, from Gelidibacter salicanalis PAMC21136.

Pardhe, B.D.Lee, M.J.Lee, J.H.Do, H.Oh, T.J.

(2023) Sci Rep 13: 17854-17854

  • DOI: https://doi.org/10.1038/s41598-023-44968-w
  • Primary Citation of Related Structures:  
    8K40, 8K41

  • PubMed Abstract: 

    Heavy metals, including mercury, are non-biodegradable and highly toxic to microorganisms even at low concentrations. Understanding the mechanisms underlying the environmental adaptability of microorganisms with Hg resistance holds promise for their use in Hg bioremediation. We characterized GbsMerA, a mercury reductase belonging to the mercury-resistant operon of Gelidibacter salicanalis PAMC21136, and found its maximum activity of 474.7 µmol/min/mg in reducing Hg +2 . In the presence of Ag and Mn, the enzyme exhibited moderate activity as 236.5 µmol/min/mg and 69 µmol/min/mg, respectively. GbsMerA exhibited optimal activity at pH 7.0 and a temperature of 60 °C. Moreover, the crystal structure of GbsMerA and structural comparison with homologues indicated that GbsMerA contains residues, Tyr437´ and Asp47, which may be responsible for metal transfer at the si-face by providing a hydroxyl group (-OH) to abstract a proton from the thiol group of cysteine. The complex structure with NADPH indicated that Y174 in the re-face can change its side chain direction upon NADPH binding, indicating that Y174 may have a role as a gate for NADPH binding. Moreover, the heterologous host expressing GbsMerA (pGbsMerA) is more resistant to Hg toxicity when compared to the host lacking GbsMerA. Overall, this study provides a background for understanding the catalytic mechanism and Hg detoxification by GbsMerA and suggests the application of genetically engineered E. coli strains for environmental Hg removal.


  • Organizational Affiliation

    Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, 31460, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)/FAD-dependent oxidoreductase
A, B
456Gelidibacter salicanalisMutation(s): 0 
Gene Names: JEM65_00875
UniProt
Find proteins for A0A934NG65 (Gelidibacter salicanalis)
Explore A0A934NG65 
Go to UniProtKB:  A0A934NG65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A934NG65
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.19α = 90
b = 105.82β = 90
c = 126.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-05-15 
  • Deposition Author(s): Do, H.

Funding OrganizationLocationGrant Number
Other governmentKorea, Republic OfPM23030

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release