3WLI

Crystal Structure Analysis of Plant Exohydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    3WLP, 3WLQ, 3WLR, 3WLH, 3WLI, 3WLJ, 3WLK, 3WLL, 3WLM, 3WLN

  • 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 ExoIA609Hordeum 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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
R [auth A], S [auth A], T [auth A], U [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [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],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.147 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.218α = 90
b = 99.218β = 90
c = 183.455γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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