4HAP

Crystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance

Kern, M.McGeehan, J.E.Streeter, S.D.Martin, R.N.Besser, K.Elias, L.Eborall, W.Malyon, G.P.Payne, C.M.Himmel, M.E.Schnorr, K.Beckham, G.T.Cragg, S.M.Bruce, N.C.McQueen-Mason, S.J.

(2013) Proc.Natl.Acad.Sci.USA 110: 10189-10194

  • DOI: 10.1073/pnas.1301502110
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Nature uses a diversity of glycoside hydrolase (GH) enzymes to convert polysaccharides to sugars. As lignocellulosic biomass deconstruction for biofuel production remains costly, natural GH diversity offers a starting point for developing industrial ...

    Nature uses a diversity of glycoside hydrolase (GH) enzymes to convert polysaccharides to sugars. As lignocellulosic biomass deconstruction for biofuel production remains costly, natural GH diversity offers a starting point for developing industrial enzymes, and fungal GH family 7 (GH7) cellobiohydrolases, in particular, provide significant hydrolytic potential in industrial mixtures. Recently, GH7 enzymes have been found in other kingdoms of life besides fungi, including in animals and protists. Here, we describe the in vivo spatial expression distribution, properties, and structure of a unique endogenous GH7 cellulase from an animal, the marine wood borer Limnoria quadripunctata (LqCel7B). RT-quantitative PCR and Western blot studies show that LqCel7B is expressed in the hepatopancreas and secreted into the gut for wood degradation. We produced recombinant LqCel7B, with which we demonstrate that LqCel7B is a cellobiohydrolase and obtained four high-resolution crystal structures. Based on a crystallographic and computational comparison of LqCel7B to the well-characterized Hypocrea jecorina GH7 cellobiohydrolase, LqCel7B exhibits an extended substrate-binding motif at the tunnel entrance, which may aid in substrate acquisition and processivity. Interestingly, LqCel7B exhibits striking surface charges relative to fungal GH7 enzymes, which likely results from evolution in marine environments. We demonstrate that LqCel7B stability and activity remain unchanged, or increase at high salt concentration, and that the L. quadripunctata GH mixture generally contains cellulolytic enzymes with highly acidic surface charge compared with enzymes derived from terrestrial microbes. Overall, this study suggests that marine cellulases offer significant potential for utilization in high-solids industrial biomass conversion processes.


    Related Citations: 
    • Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes.
      King, A.J.,Cragg, S.M.,Li, Y.,Dymond, J.,Guille, M.J.,Bowles, D.J.,Bruce, N.C.,Graham, I.A.,McQueen-Mason, S.J.
      (2010) Proc.Natl.Acad.Sci.USA 107: 5345


    Organizational Affiliation

    Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GH7 family protein
A, B
431Limnoria quadripunctataMutation(s): 0 
Gene Names: GH7B
Find proteins for D4HRL0 (Limnoria quadripunctata)
Go to UniProtKB:  D4HRL0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CBI
Query on CBI

Download SDF File 
Download CCD File 
A, B
CELLOBIOSE
C12 H22 O11
GUBGYTABKSRVRQ-QRZGKKJRSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A, B
L-PEPTIDE LINKINGC5 H7 N O3GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CBIKi: 1400000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.144 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 52.260α = 94.26
b = 54.190β = 96.02
c = 72.450γ = 94.99
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
GDAdata collection
REFMACrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references