5M16

Structure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a hydrolysed cyclopropyl carbasugar.

• PDB DOI: https://doi.org/10.2210/pdb5M16/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-07 Released: 2016-11-09 
• Deposition Author(s): Pengelly, R., Gloster, T.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.198 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars.

Adamson, C., Pengelly, R.J., Shamsi Kazem Abadi, S., Chakladar, S., Draper, J., Britton, R., Gloster, T.M., Bennet, A.J.

(2016) Angew Chem Int Ed Engl 55: 14978-14982

• PubMed: 27783466 
• DOI: https://doi.org/10.1002/anie.201607431
• Primary Citation of Related Structures:  
  5M0X, 5M12, 5M16, 5M1I


• PubMed Abstract: 
  

  Glycoside hydrolases (GHs) have attracted considerable attention as targets for therapeutic agents, and thus mechanism-based inhibitors are of great interest. We report the first structural analysis of a carbocyclic mechanism-based GH inactivator, the results of which show that the two Michaelis complexes are in ² H ₃ conformations. We also report the synthesis and reactivity of a fluorinated analogue and the structure of its covalently linked intermediate (flattened ² H ₃ half-chair). We conclude that these inactivator reactions mainly involve motion of the pseudo-anomeric carbon atom, knowledge that should stimulate the design of new transition-state analogues for use as chemical biology tools.

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Organizational Affiliation: 

Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.6 kDa 
• Atom Count: 4,796 
• Modelled Residue Count: 533 
• Deposited Residue Count: 575 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase	A	575	Thermotoga maritima	Mutation(s): 0  Gene Names: galA EC: 3.2.1.22
UniProt
Find proteins for G4FEF4 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore G4FEF4  Go to UniProtKB:  G4FEF4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7D2	E [auth A]	(1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol C8 H14 O5 ULOOKVKTDMQWTG-JMELQFKFSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.198 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.3	α = 90
b = 96.02	β = 90
c = 98.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Pengelly, R., Gloster, T.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2016-11-30
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description