1BCX

MUTATIONAL AND CRYSTALLOGRAPHIC ANALYSES OF THE ACTIVE SITE RESIDUES OF THE BACILLUS CIRCULANS XYLANASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation 3D Report Full Report



Literature

Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase.

Wakarchuk, W.W.Campbell, R.L.Sung, W.L.Davoodi, J.Yaguchi, M.

(1994) Protein Sci 3: 467-475

  • DOI: 10.1002/pro.5560030312
  • Primary Citation of Related Structures:  
    1BCX

  • PubMed Abstract: 
  • Using site-directed mutagenesis we have investigated the catalytic residues in a xylanase from Bacillus circulans. Analysis of the mutants E78D and E172D indicated that mutations in these conserved residues do not grossly alter the structure of the e ...

    Using site-directed mutagenesis we have investigated the catalytic residues in a xylanase from Bacillus circulans. Analysis of the mutants E78D and E172D indicated that mutations in these conserved residues do not grossly alter the structure of the enzyme and that these residues participate in the catalytic mechanism. We have now determined the crystal structure of an enzyme-substrate complex to 108 A resolution using a catalytically incompetent mutant (E172C). In addition to the catalytic residues, Glu 78 and Glu 172, we have identified 2 tyrosine residues, Tyr 69 and Tyr 80, which likely function in substrate binding, and an arginine residue, Arg 112, which plays an important role in the active site of this enzyme. On the basis of our work we would propose that Glu 78 is the nucleophile and that Glu 172 is the acid-base catalyst in the reaction.


    Organizational Affiliation

    Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
XYLANASEA185Bacillus circulansMutation(s): 0 
Gene Names: xlnA
EC: 3.2.1.8
Find proteins for P09850 (Bacillus circulans)
Explore P09850 
Go to UniProtKB:  P09850
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
B
2 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900116
Query on PRD_900116
B4beta-beta-xylobioseOligosaccharide /  Metabolism

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.09α = 90
b = 52.71β = 90
c = 78.97γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary