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: 1.68 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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
  • Primary Citation of Related Structures:  
    2XFG

  • 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 Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University , Ramat Aviv , Israel.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOGLUCANASE 1A466Hungateiclostridium thermocellumMutation(s): 0 
EC: 3.2.1.4
Find proteins for Q02934 (Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore Q02934 
Go to UniProtKB:  Q02934
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOGLUCANASE 1B176Hungateiclostridium thermocellumMutation(s): 0 
EC: 3.2.1.4
Find proteins for Q02934 (Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore Q02934 
Go to UniProtKB:  Q02934
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.399α = 90
b = 88.541β = 90
c = 106.486γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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