4XPV

Neutron and X-ray structure analysis of xylanase: N44D at pH6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.264 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


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
  • Primary Citation of Related Structures:  
    4S2D, 4S2F, 4S2G, 4S2H, 4XPV, 4XQ4, 4XQD, 4XQW

  • 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 of key side chains during catalysis ...

    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.


    Related Citations: 
    • Preliminary joint X-ray and neutron protein crystallographic studies of endoxylanase II from the fungus Trichoderma longibrachiatum.
      Kovalevsky, A.Y., Hanson, B.L., Seaver, S., Fisher, S.Z., Mustyakimov, M., Langan, P.
      (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 283
    • X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism.
      Wan, Q., Zhang, Q., Hamilton-Brehm, S., Weiss, K., Mustyakimov, M., Coates, L., Langan, P., Graham, D., Kovalevsky, A.
      (2014) Acta Crystallogr D Biol Crystallogr 70: 11
    • Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants.
      Wan, Q., Kovalevsky, A., Zhang, Q., Hamilton-Brehm, S., Upton, R., Weiss, K.L., Mustyakimov, M., Graham, D., Coates, L., Langan, P.
      (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 320

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase 2A189Trichoderma reeseiMutation(s): 1 
Gene Names: xyn2
EC: 3.2.1.8
UniProt
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30))
Explore P36217 
Go to UniProtKB:  P36217
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36217
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.133 
  • Space Group: P 21 21 21
  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.264 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.194α = 90
b = 60.287β = 90
c = 70.52γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH-NIGMS
State Education MinistryChina2014 Scientific Research Foundation for the Returned Overseas Chinese Scholars

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-07
    Changes: Database references
  • Version 1.2: 2015-10-14
    Changes: Database references
  • Version 1.3: 2015-10-21
    Changes: Database references
  • Version 1.4: 2016-07-20
    Changes: Data collection
  • Version 1.5: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 2.0: 2018-04-25
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-12-25
    Changes: Author supporting evidence