6MD6

CRYSTAL STRUCTURE ANALYSIS OF PLANT EXOHYDROLASE IN COMPLEX WITH METHYL 2-THIO-BETA-SOPHOROSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site.

Streltsov, V.A.Luang, S.Peisley, A.Varghese, J.N.Ketudat Cairns, J.R.Fort, S.Hijnen, M.Tvaroska, I.Arda, A.Jimenez-Barbero, J.Alfonso-Prieto, M.Rovira, C.Mendoza, F.Tiessler-Sala, L.Sanchez-Aparicio, J.E.Rodriguez-Guerra, J.Lluch, J.M.Marechal, J.D.Masgrau, L.Hrmova, M.

(2019) Nat Commun 10: 2222-2222

  • DOI: 10.1038/s41467-019-09691-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-co ...

    Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-D-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases.


    Organizational Affiliation

    School of Life Sciences, Huaiyin Normal University, Huaian, 223300, China. maria.hrmova@adelaide.edu.au.,Departamento de Ciencias Químicas, Universidad Andrés Bello, Sede Concepción, Talcahuano, 4260000, Chile.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, 08010, Spain.,School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond South Australia, 5064, Australia. maria.hrmova@adelaide.edu.au.,Institute of Chemical Research of Catalonia, The Barcelona Institute of Science and Technology, Tarragona, 43007, Spain.,Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Commonwealth Scientific and Industrial Research Organisation, Materials Science and Engineering, Parkville Victoria, 3052, Australia.,School of Chemistry and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.,Institute of Chemistry, Slovak Academy of Sciences, Bratislava, 84538, Slovak Republic.,University Grenoble Alpes, Centre de Recherches sur les Macromolécules Végétales, Grenoble cedex 9, 38041, France.,School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond South Australia, 5064, Australia.,Centre for Cooperative Research in Biosciences, Derio-Bizkaia, 48160, Spain.,Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Química Inorgànica i Orgànica, Universitat de Barcelona, Barcelona, 08028, Spain.,GE Healthcare Life Sciences, Paramatta NSW, 2150, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-D-glucan exohydrolase isoenzyme ExoI
A
609Hordeum vulgare subsp. vulgareMutation(s): 1 
Find proteins for A0A287SCR5 (Hordeum vulgare subsp. vulgare)
Go to UniProtKB:  A0A287SCR5
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
JSV
Query on JSV

Download SDF File 
Download CCD File 
A
methyl 2-S-beta-D-glucopyranosyl-2-thio-beta-D-glucopyranoside
METHYL 2-THIO-BETA-SOPHOROSIDE
C13 H24 O10 S
WAYOKHSZGNFKSX-VHGSIDFWSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.132 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.311α = 90.00
b = 100.311β = 90.00
c = 182.153γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references