3WLN

Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme EXO1 in complex with octyl-S-glucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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:  
    6MD6, 6MI1, 3WLP, 3WLQ, 3WLR, 3WLH, 3WLI, 3WLJ, 3WLK, 3WLL, 3WLM, 3WLN, 3WLO

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-D-glucan exohydrolase isoenzyme ExoIA605Hordeum vulgare subsp. vulgareMutation(s): 0 
EC: 3.2.1
UniProt
Find proteins for Q9XEI3 (Hordeum vulgare subsp. vulgare)
Explore Q9XEI3 
Go to UniProtKB:  Q9XEI3
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G93227IM
GlyCosmos:  G93227IM
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranoseD4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G18638YB
GlyCosmos:  G18638YB
GlyGen:  G18638YB
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SOG (Subject of Investigation/LOI)
Query on SOG

Download Ideal Coordinates CCD File 
E [auth A]octyl 1-thio-beta-D-glucopyranoside
C14 H28 O5 S
CGVLVOOFCGWBCS-RGDJUOJXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.703α = 90
b = 100.703β = 90
c = 181.878γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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: Data collection, Database references
  • Version 1.3: 2020-06-24
    Changes: Advisory, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary