PDBsum entry 6kwc

Hydrolase

PDB id: 6kwc

Contents

Protein chain

191 a.a.

Ligands

GOL

Metals

IOD ×4

Waters ×260

PDB id:

6kwc

Name:

Hydrolase

Title:

Crystal structure analysis of endo-beta-1,4-xylanase ii

Structure:

Endo-1,4-beta-xylanase 2. Chain: a. Synonym: xylanase 2,1,4-beta-d-xylan xylanohydrolase 2,alkaline endo- beta-1,4-xylanase. Engineered: yes. Mutation: yes

Source:

Trichoderma reesei rut c-30. Hypocrea jecorina rut c-30. Organism_taxid: 1344414. Gene: xyn2, m419draft_124931. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.30Å R-factor: 0.158 R-free: 0.172

Authors:

C.Li,Q.Wan

Key ref:

Z.Li et al. (2020). Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography. Protein J, 39, 671-680. PubMed id: 33128114 DOI: 10.1016/j.polymdegradstab.2011.01.010

Date:

06-Sep-19 Release date: 27-Jan-21

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: 191 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

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: 10.1016/j.polymdegradstab.2011.01.010

Protein J 39:671-680 (2020)

PubMed id: 33128114

Studying the Role of a Single Mutation of a Family 11 Glycoside Hydrolase Using High-Resolution X-ray Crystallography.

Z.Li, X.Zhang, C.Li, A.Kovalevsky, Q.Wan.

ABSTRACT

XynII is a family 11 glycoside hydrolase that uses the retaining mechanism for catalysis. In the active site, E177 works as the acid/base and E86 works as the nucleophile. Mutating an uncharged residue (N44) to an acidic residue (D) near E177 decreases the enzyme's optimal pH by ~ 1.0 unit. D44 was previously suggested to be a second proton carrier for catalysis. To test this hypothesis, we abolished the activity of E177 by mutating it to be Q, and mutated N44 to be D or E. These double mutants have dramatically decreased activities. Our high-resolution crystallographic structures and the microscopic pK_a calculations show that D44 has similar position and pK_a value during catalysis, indicating that D44 changes electrostatics around E177, which makes it prone to rotate as the acid/base in acidic conditions, thus decreases the pH optimum. Our results could be helpful to design enzymes with different pH optimum.