Crystal Structure Analysis of Plant Exohydrolase

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

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This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1038/s41467-019-09691-z
  • Primary Citation of Related Structures:  
    3WLH, 3WLI, 3WLJ, 3WLK, 3WLL, 3WLM, 3WLN, 3WLO, 3WLP, 3WLQ, 3WLR, 6MD6, 6MI1

  • 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-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

    Commonwealth Scientific and Industrial Research Organisation, Materials Science and Engineering, Parkville Victoria, 3052, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-D-glucan exohydrolase isoenzyme ExoI609Hordeum vulgare subsp. vulgareMutation(s): 2 
EC: 3.2.1
Find proteins for Q9XEI3 (Hordeum vulgare subsp. vulgare)
Explore Q9XEI3 
Go to UniProtKB:  Q9XEI3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XEI3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
C8 H15 N O6
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.781α = 90
b = 100.781β = 90
c = 183.159γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2019-11-20
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary