5ZQX

Crystal structure of beta-xylosidase mutant (E186Q) from Bacillus pumilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based protein engineering of bacterial beta-xylosidase to increase the production yield of xylobiose from xylose

Hong, S.Kyung, M.Jo, I.Kim, Y.R.Ha, N.C.

(2018) Biochem. Biophys. Res. Commun. 501: 703-710

  • DOI: 10.1016/j.bbrc.2018.05.051
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Xylobiose consists of two molecules of xylose and has been highly recognized as a food supplement because it possesses high prebiotic functions. β-xylosidase exhibits enzymatic activity to hydrolyze xylobiose, and the enzyme can also catalyze the rev ...

    Xylobiose consists of two molecules of xylose and has been highly recognized as a food supplement because it possesses high prebiotic functions. β-xylosidase exhibits enzymatic activity to hydrolyze xylobiose, and the enzyme can also catalyze the reverse reaction in the presence of high concentrations of xylose. Previously, β-xylosidase from Bacillus pumilus IPO (BpXynB), belonging to GH family 43, was employed to produce xylobiose from xylose. To improve the enzymatic efficiency, this study determined the high-resolution structure of BpXynB in a complex with xylobiose and engineered BpXynB based on the structures. The structure of BpXynB deciphered the residues involved in the recognition of the xylobiose. A site-directed mutation at the residue for xylobiose recognition increased the yield of xylobiose by 20% compared to a similar activity of the wild type enzyme. The complex structure of the mutant enzyme and xylobiose provided the structural basis for a higher yield of the engineered protein. This engineered enzyme would enable a higher economic production of xylobiose, and a similar engineering strategy could be applied within the same family of enzymes.


    Organizational Affiliation

    Center for Food and Bioconvergence, Department of Biosystems & Biomaterials Science and Engineering, College of Agriculture and Life Sciences (CALS), Seoul National University, Seoul, 08826, Republic of Korea; R&D Center, TS Corporation, 116, Incheon, 22300, Republic of Korea.,Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Department of Agicultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Center for Food and Bioconvergence, Department of Biosystems & Biomaterials Science and Engineering, College of Agriculture and Life Sciences (CALS), Seoul National University, Seoul, 08826, Republic of Korea.,Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Department of Agicultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. Electronic address: hanc210@snu.ac.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-xylosidase
A, B, C, D
541Bacillus pumilusMutation(s): 1 
Gene Names: xynB
EC: 3.2.1.37
Find proteins for P07129 (Bacillus pumilus)
Go to UniProtKB:  P07129
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXP
Query on BXP

Download SDF File 
Download CCD File 
A, B, C, D
4-O-beta-D-xylopyranosyl-beta-D-xylopyranose
XYLOBIOSE
C10 H18 O9
LGQKSQQRKHFMLI-SJYYZXOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 103.259α = 90.00
b = 104.776β = 111.13
c = 113.163γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references