4S2H

Joint X-ray/neutron structure of Trichoderma reesei xylanase II at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.199 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report



Literature

Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.

Wan, Q.Parks, J.M.Hanson, B.L.Fisher, S.Z.Ostermann, A.Schrader, T.E.Graham, D.E.Coates, L.Langan, P.Kovalevsky, A.

(2015) Proc Natl Acad Sci U S A 112: 12384-12389

  • DOI: 10.1073/pnas.1504986112
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values ...

    Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD=pH+0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.


    Organizational Affiliation

    Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 kovalevskyay@ornl.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase 2
A
190Trichoderma reeseiMutation(s): 0 
EC: 3.2.1.8
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30))
Go to UniProtKB:  P36217
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
  • Method: NEUTRON DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.261 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.613α = 90
b = 60.033β = 90
c = 70.553γ = 90
Software Package:
Software NamePurpose
nCNSrefinement
HKL-2000data collection
d*TREKdata scaling
HKL-2000data reduction
d*TREKdata reduction
LAUENORMdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Database references
  • Version 1.3: 2015-12-02
    Changes: Atomic model
  • Version 1.4: 2018-04-25
    Changes: Data collection
  • Version 2.0: 2019-12-25
    Changes: Derived calculations, Polymer sequence