PDBsum entry 4xqw

Hydrolase

PDB id: 4xqw

Contents

Protein chain

189 a.a.

Ligands

MES

Metals

IOD ×5

Waters ×234

PDB id:

4xqw

Name:

Hydrolase

Title:

X-ray structure analysis of xylanase-n44e with mes at ph6.0

Structure:

Endo-1,4-beta-xylanase 2. Chain: a. Fragment: substrate-binding groove, jelly roll. Synonym: xylanase 2,1,4-beta-d-xylan xylanohydrolase 2. Engineered: yes

Source:

Hypocrea jecorina. Organism_taxid: 51453. Gene: xyn2. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.50Å R-factor: 0.174 R-free: 0.179

Authors:

Q.Wan,J.M.Park,D.M.Riccardi,L.B.Hanson,Z.Fisher,J.C.Smith, A.Ostermann,T.Schrader,D.E.Graham,L.Coates,P.Langan,A.Y.Kovalevsky

Key ref:

Q.Wan et al. (2015). Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Proc Natl Acad Sci U S A, 112, 12384-12389. PubMed id: 26392527 DOI: 10.1073/pnas.1504986112

Date:

20-Jan-15 Release date: 23-Sep-15

Protein chain

P36217  (XYN2_HYPJR) -  Endo-1,4-beta-xylanase 2 from Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)

Seq: 223 a.a.

Struc: 189 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.8 - endo-1,4-beta-xylanase.
• Reaction: Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.

DOI no: 10.1073/pnas.1504986112

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

PubMed id: 26392527

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

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

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.