4Q3M

Crystal structure of MGS-M4, an aldo-keto reductase enzyme from a Medee basin deep-sea metagenome library


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.552 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.

Alcaide, M.Stogios, P.J.Lafraya, A.Tchigvintsev, A.Flick, R.Bargiela, R.Chernikova, T.N.Reva, O.N.Hai, T.Leggewie, C.C.Katzke, N.La Cono, V.Matesanz, R.Jebbar, M.Jaeger, K.E.Yakimov, M.M.Yakunin, A.F.Golyshin, P.N.Golyshina, O.V.Savchenko, A.Ferrer, M.

(2015) Environ Microbiol 17: 332-345

  • DOI: 10.1111/1462-2920.12660
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The present study provides a deeper view of protein functionality as a function of temperature, salt and pressure in deep-sea habitats. A set of eight different enzymes from five distinct deep-sea (3040-4908 m depth), moderately warm (14.0-16.5°C) bi ...

    The present study provides a deeper view of protein functionality as a function of temperature, salt and pressure in deep-sea habitats. A set of eight different enzymes from five distinct deep-sea (3040-4908 m depth), moderately warm (14.0-16.5°C) biotopes, characterized by a wide range of salinities (39-348 practical salinity units), were investigated for this purpose. An enzyme from a 'superficial' marine hydrothermal habitat (65°C) was isolated and characterized for comparative purposes. We report here the first experimental evidence suggesting that in salt-saturated deep-sea habitats, the adaptation to high pressure is linked to high thermal resistance (P value = 0.0036). Salinity might therefore increase the temperature window for enzyme activity, and possibly microbial growth, in deep-sea habitats. As an example, Lake Medee, the largest hypersaline deep-sea anoxic lake of the Eastern Mediterranean Sea, where the water temperature is never higher than 16°C, was shown to contain halopiezophilic-like enzymes that are most active at 70°C and with denaturing temperatures of 71.4°C. The determination of the crystal structures of five proteins revealed unknown molecular mechanisms involved in protein adaptation to poly-extremes as well as distinct active site architectures and substrate preferences relative to other structurally characterized enzymes.


    Organizational Affiliation

    Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28049, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MGS-M4
A, B, C, D, E, F
274Firmicutes bacterium enrichment culture clone fosmid MGS-M2Mutation(s): 0 
Find proteins for A0A0B5KNF6 (Firmicutes bacterium enrichment culture clone fosmid MGS-M2)
Go to UniProtKB:  A0A0B5KNF6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.552 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.207 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 172.469α = 90.00
b = 172.469β = 90.00
c = 113.055γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-3000data scaling
PHENIXrefinement
HKL-3000data reduction
StructureStudiodata collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-25
    Type: Initial release
  • Version 1.1: 2015-03-18
    Type: Database references