Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from a Lake Matapan deep-sea metagenome library

Experimental Data Snapshot

  • Resolution: 1.74 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1111/1462-2920.12660
  • Primary Citation of Related Structures:  
    4Q3K, 4Q3L, 4Q3M, 4Q3N, 4Q3O

  • 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) 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H
348unidentifiedMutation(s): 0 
Gene Names: MGS-MT1
Find proteins for A0A0B5KQQ5 (uncultured Gammaproteobacteria bacterium)
Explore A0A0B5KQQ5 
Go to UniProtKB:  A0A0B5KQQ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B5KQQ5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MES

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
OA [auth G]
PA [auth G]
Q [auth B]
K [auth A],
L [auth A],
OA [auth G],
PA [auth G],
Q [auth B],
RA [auth H],
SA [auth H],
T [auth C],
U [auth C],
Z [auth D]
C6 H13 N O4 S
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
IA [auth E],
JA [auth E],
LA [auth F],
M [auth A],
MA [auth F],
N [auth A],
O [auth A],
QA [auth G],
R [auth B],
V [auth C],
W [auth C],
X [auth C]
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
FA [auth D]
GA [auth E]
HA [auth E]
I [auth A]
J [auth A]
FA [auth D],
GA [auth E],
HA [auth E],
I [auth A],
J [auth A],
KA [auth F],
NA [auth G],
P [auth B],
S [auth C],
Y [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.74 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.454α = 90
b = 131.397β = 103.55
c = 112.441γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description