5XC8

Crystal structure of GH45 endoglucanase EG27II at pH5.5, in complex with cellobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.107 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean.

Nomura, T.Iwase, H.Saka, N.Takahashi, N.Mikami, B.Mizutani, K.

(2019) Acta Crystallogr D Struct Biol 75: 426-436

  • DOI: 10.1107/S2059798319003000
  • Primary Citation of Related Structures:  
    5XBX, 5XC9, 5XC8, 5XC4, 5XBU, 5XCA

  • PubMed Abstract: 
  • Although endogenous animal cellulases have great potential for industrial applications such as bioethanol production, few investigations have focused on these enzymes. In this study, the glycoside hydrolase family 45 (GH45) subfamily B endoglucanase EG27II from the snail Ampullaria crossean was expressed using a Pichia pastoris expression system and the crystal structure of the apo form was determined at 1 ...

    Although endogenous animal cellulases have great potential for industrial applications such as bioethanol production, few investigations have focused on these enzymes. In this study, the glycoside hydrolase family 45 (GH45) subfamily B endoglucanase EG27II from the snail Ampullaria crossean was expressed using a Pichia pastoris expression system and the crystal structure of the apo form was determined at 1.00 Å resolution; this is the highest resolution structure of an animal endoglucanase. The results showed that EG27II has a double-ψ six-stranded β-barrel and that the structure of EG27II more closely resembles those of subfamily C enzymes than those of subfamily A enzymes. The structure of EG27II complexed with cellobiose was also determined under cryoconditions and at room temperature at three pH values, pH 4.0, 5.5 and 8.0, and no structural changes were found to be associated with the change in pH. The structural comparison and catalytic activity measurements showed that Asp137 and Asn112 function as the catalytic acid and base, respectively, and that Asp27 is also an important residue for catalysis. These high-resolution structures of EG27II provide a large amount of information for structure-based enzyme modification and cell-surface engineering, which will advance biofuel production using animal-derived cellulases.


    Organizational Affiliation

    Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-beta-1,4-glucanaseA190Ampullaria crosseanMutation(s): 0 
Gene Names: EG27II
EC: 3.2.1.4
UniProt
Find proteins for A7KMF0 (Ampullaria crossean)
Explore A7KMF0 
Go to UniProtKB:  A7KMF0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranoseB, C2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84824ZO
GlyCosmos:  G84824ZO
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900005
Query on PRD_900005
B, Cbeta-cellobioseOligosaccharide /  Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.138 
  • R-Value Work: 0.105 
  • R-Value Observed: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.853α = 90
b = 47.309β = 90
c = 93.081γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan society for the promotion scienceJapan25450126

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary