8C10 | pdb_00008c10

Biochemical and structural characterisation of an alkaline family GH5 cellulase from a shipworm symbiont


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.133 (Depositor), 0.132 (DCC) 
  • R-Value Work: 
    0.112 (Depositor), 0.112 (DCC) 
  • R-Value Observed: 
    0.113 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8C10

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Biochemical and structural characterisation of a family GH5 cellulase from endosymbiont of shipworm P. megotara.

Junghare, M.Manavalan, T.Fredriksen, L.Leiros, I.Altermark, B.Eijsink, V.G.H.Vaaje-Kolstad, G.

(2023) Biotechnol Biofuels Bioprod 16: 61-61

  • DOI: https://doi.org/10.1186/s13068-023-02307-1
  • Primary Citation Related Structures: 
    8C10

  • PubMed Abstract: 

    Cellulases play a key role in the enzymatic conversion of plant cell-wall polysaccharides into simple and economically relevant sugars. Thus, the discovery of novel cellulases from exotic biological niches is of great interest as they may present properties that are valuable in the biorefining of lignocellulosic biomass. We have characterized a glycoside hydrolase 5 (GH5) domain of a bi-catalytic GH5-GH6 multi-domain enzyme from the unusual gill endosymbiont Teredinibacter waterburyi of the wood-digesting shipworm Psiloteredo megotara. The catalytic GH5 domain, was cloned and recombinantly produced with or without a C-terminal family 10 carbohydrate-binding module (CBM). Both variants showed hydrolytic endo-activity on soluble substrates such as β-glucan, carboxymethylcellulose and konjac glucomannan, respectively. However, low activity was observed towards the crystalline form of cellulose. Interestingly, when co-incubated with a cellulose-active LPMO, a clear synergy was observed that boosted the overall hydrolysis of crystalline cellulose. The crystal structure of the GH5 catalytic domain was solved to 1.0 Å resolution and revealed a substrate binding cleft extension containing a putative + 3 subsite, which is uncommon in this enzyme family. The enzyme was active in a wide range of pH, temperatures and showed high tolerance for NaCl. This study provides significant knowledge in the discovery of new enzymes from shipworm gill endosymbionts and sheds new light on biochemical and structural characterization of cellulolytic cellulase. Study demonstrated a boost in the hydrolytic activity of cellulase on crystalline cellulose when co-incubated with cellulose-active LPMO. These findings will be relevant for the development of future enzyme cocktails that may be useful for the biotechnological conversion of lignocellulose.


  • Organizational Affiliation
    • Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway. madan.junghare@nmbu.no.

Macromolecule Content 

  • Total Structure Weight: 35.61 kDa 
  • Atom Count: 2,799 
  • Modeled Residue Count: 297 
  • Deposited Residue Count: 321 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GH5 Cellulase321Teredinibacter waterburyiMutation(s): 0 
UniProt
Find proteins for A0AA82WPD7 (Teredinibacter waterburyi)
Explore A0AA82WPD7 
Go to UniProtKB:  A0AA82WPD7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WPD7
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
(Subject of Investigation/LOI)

Query on TRS



Download:Ideal Coordinates CCD File
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
(Subject of Investigation/LOI)

Query on K



Download:Ideal Coordinates CCD File
G [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.133 (Depositor), 0.132 (DCC) 
  • R-Value Work:  0.112 (Depositor), 0.112 (DCC) 
  • R-Value Observed: 0.113 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.041α = 90
b = 68.426β = 90
c = 87.188γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection