1BYH

MOLECULAR AND ACTIVE-SITE STRUCTURE OF A BACILLUS (1-3,1-4)-BETA-GLUCANASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Molecular and active-site structure of a Bacillus 1,3-1,4-beta-glucanase.

Keitel, T.Simon, O.Borriss, R.Heinemann, U.

(1993) Proc Natl Acad Sci U S A 90: 5287-5291

  • DOI: 10.1073/pnas.90.11.5287
  • Primary Citation of Related Structures:  
    1BYH

  • PubMed Abstract: 
  • The three-dimensional structure of the hybrid Bacillus 1,3-1,4-beta-glucanase (beta-glucanase; 1,3-1,4-beta-D-glucan 4-glucanohydrolase, lichenase, EC 3.2.1.73) designated H(A16-M) was determined by x-ray crystallography at a resolution of 2.0 A and refined to an R value of 16 ...

    The three-dimensional structure of the hybrid Bacillus 1,3-1,4-beta-glucanase (beta-glucanase; 1,3-1,4-beta-D-glucan 4-glucanohydrolase, lichenase, EC 3.2.1.73) designated H(A16-M) was determined by x-ray crystallography at a resolution of 2.0 A and refined to an R value of 16.4% using stereochemical restraints. The protein molecule consists mainly of two seven-stranded antiparallel beta-pleated sheets arranged atop each other to form a compact, sandwich-like structure. A channel crossing one side of the protein molecule accommodates an inhibitor, 3,4-epoxybutyl beta-D-cellobioside, which binds covalently to the side chain of Glu-105, as seen in a crystal structure analysis at 2.8-A resolution of the protein-inhibitor complex (R = 16.8%). That Glu-105 may be indispensible for enzyme catalysis by H(A16-M) is suggested by site-directed mutagenesis of this residue, which inevitably leads to an inactive enzyme.


    Related Citations: 
    • Hybrid Bacillus (1-3,1-4)-Beta-Glucanase: Engineering Thermostable Enzymes by Construction of Hybrid Genes
      Olsen, O., Borriss, R., Simon, O., Thomsen, K.
      (1991) Mol Gen Genet 225: 177

    Organizational Affiliation

    Institut für Kristallographie, Freie Universität, Berlin, Federal Republic of Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYBRIDA214synthetic constructMutation(s): 0 
EC: 3.2.1.73
UniProt
Find proteins for P23904 (Paenibacillus macerans)
Explore P23904 
Go to UniProtKB:  P23904
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranoseB2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84824ZO
GlyCosmos:  G84824ZO
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NBU
Query on NBU

Download Ideal Coordinates CCD File 
D [auth A]N-BUTANE
C4 H10
IJDNQMDRQITEOD-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900005
Query on PRD_900005
Bbeta-cellobioseOligosaccharide /  Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.32α = 90
b = 78.52β = 90
c = 39.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    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, Derived calculations, Structure summary