8QQH | pdb_00008qqh

Structure of beta-galactosidase from Desulfurococcus amyloliticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.211 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.175 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8QQH

This is version 1.2 of the entry. See complete history

Literature

The archaeal highly thermostable GH35 family beta-galactosidase Da beta Gal has a unique seven domain protein fold.

Kil, Y.Pichkur, E.B.Sergeev, V.R.Zabrodskaya, Y.Myasnikov, A.Konevega, A.L.Shtam, T.Samygina, V.R.Rychkov, G.N.

(2024) FEBS J 291: 3686-3705

  • DOI: https://doi.org/10.1111/febs.17166
  • Primary Citation Related Structures: 
    8QQH

  • PubMed Abstract: 

    The most extensively studied β-d-galactosidases (EC3.2.1.23) belonging to four glycoside hydrolase (GH) families 1, 2, 35, and 42 are widely distributed among Bacteria, Archaea and Eukaryotes. Here, we report a novel GH35 family β-galactosidase from the hyperthermophilic Thermoprotei archaeon Desulfurococcus amylolyticus (DaβGal). Unlike fungal monomeric six-domain β-galactosidases, the DaβGal enzyme is a dimer; it has an extra jelly roll domain D7 and three composite domains (D4, D5, and D6) that are formed by the distantly located polypeptide chain regions. The enzyme possesses a high specificity for β-d-galactopyranosides, and its distinguishing feature is the ability to cleave pNP-β-d-fucopyranoside. DaβGal efficiently catalyzes the hydrolysis of lactose at high temperatures, remains stable and active at 65 °С, and retains activity at 95 °С with a half-life time value equal to 73 min. These properties make archaeal DaβGal a more attractive candidate for biotechnology than the widely used fungal β-galactosidases.


  • Organizational Affiliation
    • Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute named by B.P.Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.

Macromolecule Content 

  • Total Structure Weight: 226.49 kDa 
  • Atom Count: 16,160 
  • Modeled Residue Count: 1,940 
  • Deposited Residue Count: 1,976 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-galactosidaseA [auth AAA],
B [auth BBB]
988Desulfurococcus amylolyticusMutation(s): 0 
Gene Names: DKAM_0402
UniProt
Find proteins for B8D3P7 (Desulfurococcus amylolyticus (strain DSM 18924 / JCM 16383 / VKM B-2413 / 1221n))
Explore B8D3P7 
Go to UniProtKB:  B8D3P7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8D3P7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.211 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.175 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.227α = 90
b = 140.763β = 90
c = 207.773γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentRussian Federation--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary