5AXH

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus

Suzuki, N.Kishine, N.Fujimoto, Z.Sakurai, M.Momma, M.Ko, J.A.Nam, S.H.Kimura, A.Kim, Y.M.

(2016) J Biochem 159: 331-339

  • DOI: https://doi.org/10.1093/jb/mvv104
  • Primary Citation of Related Structures:  
    5AXG, 5AXH

  • PubMed Abstract: 

    The crystal structures of the wild type and catalytic mutant Asp-312→Gly in complex with isomaltohexaose of endo-1,6-dextranase from the thermophilic bacterium Thermoanaerobacter pseudethanolicus (TpDex), belonging to the glycoside hydrolase family 66, were determined. TpDex consists of three structural domains, a catalytic domain comprising an (β/α)8-barrel and two β-domains located at both N- and C-terminal ends. The isomaltohexaose-complex structure demonstrated that the isomaltohexaose molecule was bound across the catalytic site, showing that TpDex had six subsites (-4 to +2) in the catalytic cleft. Marked movement of the Trp-376 side-chain along with loop 6, which was the side wall component of the cleft at subsite +1, was observed to occupy subsite +1, indicating that it might expel the cleaved aglycone subsite after the hydrolysis reaction. Structural comparison with other mesophilic enzymes indicated that several structural features of TpDex, loop deletion, salt bridge and surface-exposed charged residue, may contribute to thermostability.


  • Organizational Affiliation

    Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan; zui@affrc.go.jp u9897854@jnu.ac.kr.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dextranase
A, B
618Thermoanaerobacter pseudethanolicus ATCC 33223Mutation(s): 1 
Gene Names: Teth39_0264
EC: 3.2.1.11
UniProt
Find proteins for B0KBZ7 (Thermoanaerobacter pseudethanolicus (strain ATCC 33223 / 39E))
Explore B0KBZ7 
Go to UniProtKB:  B0KBZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0KBZ7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose
C
4N/A
Glycosylation Resources
GlyTouCan:  G80662SX
GlyCosmos:  G80662SX
GlyGen:  G80662SX
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose
D
6N/A
Glycosylation Resources
GlyTouCan:  G26640RK
GlyCosmos:  G26640RK
GlyGen:  G26640RK
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.334α = 90
b = 99.179β = 90
c = 169.254γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Agriculture, Forestry and FisheriesJapan25001A
National Research Foundation of KoreaKorea, Republic Of2010-0020141

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2016-03-09
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary