4Q3K | pdb_00004q3k

Crystal structure of MGS-M1, an alpha/beta hydrolase enzyme from a Medee basin deep-sea metagenome library


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.186 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 
    0.148 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4Q3K

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 59.09 kDa 
  • Atom Count: 4,635 
  • Modeled Residue Count: 483 
  • Deposited Residue Count: 520 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MGS-M1
A, B
260unidentifiedMutation(s): 0 
UniProt
Find proteins for A0A0B5KGV8 (Firmicutes bacterium enrichment culture clone fosmid MGS-M1)
Explore A0A0B5KGV8 
Go to UniProtKB:  A0A0B5KGV8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B5KGV8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
I [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
F

Query on F



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B]
FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.186 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.148 (DCC) 
  • R-Value Observed: 0.148 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.991α = 90
b = 82.716β = 109.32
c = 77.377γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-25
    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