5K9Y

Crystal structure of a thermophilic xylanase A from Bacillus subtilis 1A1 quadruple mutant Q7H/G13R/S22P/S179C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis.

Silva, S.B.Pinheiro, M.P.Fuzo, C.A.Silva, S.R.Ferreira, T.L.Lourenzoni, M.R.Nonato, M.C.Vieira, D.S.Ward, R.J.

(2017) Int. J. Biol. Macromol. 97: 574-584

  • DOI: 10.1016/j.ijbiomac.2017.01.054

  • PubMed Abstract: 
  • A thermostable variant of the mesophilic xylanase A from Bacillus subtilis (BsXynA-G3_4x) contains the four mutations Gln7His, Gly13Arg, Ser22Pro, and Ser179Cys. The crystal structure of the BsXynA-G3_4x has been solved, and the local environments ar ...

    A thermostable variant of the mesophilic xylanase A from Bacillus subtilis (BsXynA-G3_4x) contains the four mutations Gln7His, Gly13Arg, Ser22Pro, and Ser179Cys. The crystal structure of the BsXynA-G3_4x has been solved, and the local environments around each of these positions investigated by molecular dynamics (MD) simulations at 328K and 348K. The structural and MD simulation results were correlated with thermodynamic data of the wild-type enzyme, the 4 single mutants and the BsXynA-G3_4x. This analysis suggests that the overall stabilizing effect is entropic, and is consistent with solvation of charged residues and reduction of main-chain flexibility. Furthermore, increased protein-protein hydrogen bonding and hydrophobic interactions also contribute to stabilize the BsXynA-G3_4x. The study revealed that a combination of several factors is responsible for increased thermostability of the BsXynA-G3_4x; (i) introduction of backbone rigidity in regions of high flexibility, (ii) solvation effects and (iii) hydrophobic contacts.


    Organizational Affiliation

    Instituto de QuĂ­mica, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte 59072-970, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-xylanase A
A, B
185Bacillus subtilis (strain 168)Mutation(s): 4 
Gene Names: xynA
EC: 3.2.1.8
Find proteins for P18429 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P18429
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.178α = 90.00
b = 52.002β = 91.28
c = 72.474γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological DevelopmentBrazil473327/2013
Sao Paulo Research FoundationBrazil2007/08703-00

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Author supporting evidence
  • Version 1.2: 2019-04-17
    Type: Author supporting evidence, Data collection