6LCK | pdb_00006lck

TtGalA, alpha-galactosidase from Thermus thermophilus in complex with p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.222 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of alpha-Galactosidase fromThermus thermophilus: Insight into Hexamer Assembly and Substrate Specificity.

Chen, S.C.Wu, S.P.Chang, Y.Y.Hwang, T.S.Lee, T.H.Hsu, C.H.

(2020) J Agric Food Chem 68: 6161-6169

  • DOI: https://doi.org/10.1021/acs.jafc.0c00871
  • Primary Citation Related Structures: 
    6LCJ, 6LCK, 6LCL

  • PubMed Abstract: 

    α-Galactosidase catalyzes the hydrolysis of a terminal α-galactose residue in galacto-oligosaccharides and has potential in various industrial applications and food processing. We determined the crystal structures of α-galactosidase from the thermophilic microorganism Thermus thermophilus (TtGalA) and its complexes with pNPGal and stachyose. The monomer folds into an N-terminal domain, a catalytic (β/α) 8 barrel domain, and a C-terminal domain. The domain organization is similar to that of the other family of 36 α-galactosidases, but TtGalA presents a cagelike hexamer. Structural analysis shows that oligomerization may be a key factor for the thermal adaption of TtGalA. The structure of TtGalA complexed with stachyose reveals only the existence of one -1 subsite and one +1 subsite in the active site. Structural comparison of the stachyose-bound complexes of TtGalA and GsAgaA, a tetrameric enzyme with four subsites, suggests evolutionary divergence of substrate specificity within the GH36 family of α-galactosidases. To the best of our knowledge, the crystal structure of TtGalA is the first report of a quaternary structure as a hexameric assembly in the α-galactosidase family.


  • Organizational Affiliation
    • Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.

Macromolecule Content 

  • Total Structure Weight: 162.86 kDa 
  • Atom Count: 11,550 
  • Modeled Residue Count: 1,437 
  • Deposited Residue Count: 1,437 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-galactosidase
A, B, C
479Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHB115
UniProt
Find proteins for Q53W51 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q53W51 
Go to UniProtKB:  Q53W51
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53W51
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.222 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.631α = 90
b = 205.288β = 90
c = 163.898γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan108-2628-B-002-013
Ministry of Science and Technology (Taiwan)Taiwan108-2113-M-002-011

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2024-04-03
    Changes: Refinement description