Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.11 kDa 
• Atom Count: 1648 
• Modelled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1

4XPV

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

• PDB DOI: 10.2210/pdb4XPV/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2015-01-18 Released: 2015-09-30 
• Deposition Author(s): Wan, Q., Park, J.M., Riccardi, D.M., Hanson, L.B., Fisher, Z., Smith, J.C., Ostermann, A., Schrader, T., Graham, D.E., Coates, L., Langan, P., Kovalevsky, A.Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), State Education Ministry

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Experimental Data Snapshot

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

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

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

• PubMed: 26392527 
• 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. 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.

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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

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Organizational Affiliation: 

Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase 2	A	189	Trichoderma reesei	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B [auth A], C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

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 = 49.194	α = 90
b = 60.287	β = 90
c = 70.52	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-01-18 
• Released Date: 2015-09-30 
Deposition Author(s): Wan, Q., Park, J.M., Riccardi, D.M., Hanson, L.B., Fisher, Z., Smith, J.C., Ostermann, A., Schrader, T., Graham, D.E., Coates, L., Langan, P., Kovalevsky, A.Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIH-NIGMS
State Education Ministry	China	2014 Scientific Research Foundation for the Returned Overseas Chinese Scholars

Revision History  

• 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