2XFG

Reassembly and co-crystallization of a family 9 processive endoglucanase from separately expressed GH9 and CBM3c modules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.679 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Reassembly and Co-Crystallization of a Family 9 Processive Endoglucanase from its Component Parts: Structural and Functional Significance of Intermodular Linker

Petkun, S.Grinberg, I.R.Lamed, R.Jindou, S.Burstein, T.Yaniv, O.Shoham, Y.Shimon, J.W.L.Bayer, E.A.Frolow, F.

(2015) Peerj 3: E1126

  • DOI: 10.7717/peerj.1126

  • PubMed Abstract: 
  • Non-cellulosomal processive endoglucanase 9I (Cel9I) from Clostridium thermocellum is a modular protein, consisting of a family-9 glycoside hydrolase (GH9) catalytic module and two family-3 carbohydrate-binding modules (CBM3c and CBM3b), separated by ...

    Non-cellulosomal processive endoglucanase 9I (Cel9I) from Clostridium thermocellum is a modular protein, consisting of a family-9 glycoside hydrolase (GH9) catalytic module and two family-3 carbohydrate-binding modules (CBM3c and CBM3b), separated by linker regions. GH9 does not show cellulase activity when expressed without CBM3c and CBM3b and the presence of the CBM3c was previously shown to be essential for endoglucanase activity. Physical reassociation of independently expressed GH9 and CBM3c modules (containing linker sequences) restored 60-70% of the intact Cel9I endocellulase activity. However, the mechanism responsible for recovery of activity remained unclear. In this work we independently expressed recombinant GH9 and CBM3c with and without their interconnecting linker in Escherichia coli. We crystallized and determined the molecular structure of the GH9/linker-CBM3c heterodimer at a resolution of 1.68 Å to understand the functional and structural importance of the mutual spatial orientation of the modules and the role of the interconnecting linker during their re-association. Enzyme activity assays and isothermal titration calorimetry were performed to study and compare the effect of the linker on the re-association. The results indicated that reassembly of the modules could also occur without the linker, albeit with only very low recovery of endoglucanase activity. We propose that the linker regions in the GH9/CBM3c endoglucanases are important for spatial organization and fixation of the modules into functional enzymes.


    Organizational Affiliation

    Department of Life Sciences, Meijo University , Nagoya , Japan.,Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology , Haifa , Israel.,Department of Biological Chemistry, The Weizmann Institute of Science , Rehovot , Israel.,Department of Chemical Research Support, The Weizmann Institute of Science , Rehovot , Israel.,Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University , Ramat Aviv , Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOGLUCANASE 1
A
466Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Gene Names: celI
EC: 3.2.1.4
Find proteins for Q02934 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  Q02934
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ENDOGLUCANASE 1
B
176Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Gene Names: celI
EC: 3.2.1.4
Find proteins for Q02934 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  Q02934
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.679 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.399α = 90.00
b = 88.541β = 90.00
c = 106.486γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references, Version format compliance
  • Version 1.2: 2015-10-07
    Type: Database references
  • Version 1.3: 2016-01-13
    Type: Database references