4Q3O

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

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: 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 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MGS-MT1
A, B, C, D, E
A, B, C, D, E, F, G, H
348unidentifiedMutation(s): 0 
Gene Names: MGS-MT1
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
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]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GOL
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]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
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]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
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