5GXZ

Crystal structure of endoglucanase CelQ from Clostridium thermocellum complexed with cellobiose and cellotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal Structures of the C-Terminally Truncated Endoglucanase Cel9Q from Clostridium thermocellum Complexed with Cellodextrins and Tris.

Jeng, W.Y.Liu, C.I.Lu, T.J.Lin, H.J.Wang, N.C.Wang, A.H.

(2019) Chembiochem 20: 295-307

  • DOI: 10.1002/cbic.201800789
  • Primary Citation of Related Structures:  
    5GXY, 5GXX, 5GXZ, 5GY0, 5GY1

  • PubMed Abstract: 
  • Endoglucanase CtCel9Q is one of the enzyme components of the cellulosome, which is an active cellulase system in the thermophile Clostridium thermocellum. The precursor form of CtCel9Q comprises a signal peptide, a glycoside hydrolase family 9 catalytic domain, a type 3c carbohydrate-binding module (CBM), and a type I dockerin domain ...

    Endoglucanase CtCel9Q is one of the enzyme components of the cellulosome, which is an active cellulase system in the thermophile Clostridium thermocellum. The precursor form of CtCel9Q comprises a signal peptide, a glycoside hydrolase family 9 catalytic domain, a type 3c carbohydrate-binding module (CBM), and a type I dockerin domain. Here, we report the crystal structures of C-terminally truncated CtCel9Q (CtCel9QΔc) complexed with Tris, Tris+cellobiose, cellobiose+cellotriose, cellotriose, and cellotetraose at resolutions of 1.50, 1.70, 2.05, 2.05 and 1.75 Å, respectively. CtCel9QΔc forms a V-shaped homodimer through residues Lys529-Glu542 on the type 3c CBM, which pairs two β-strands (β4 and β5 of the CBM). In addition, a disulfide bond was formed between the two Cys535 residues of the protein monomers in the asymmetric unit. The structures allow the identification of four minus (-) subsites and two plus (+) subsites; this is important for further understanding the structural basis of cellulose binding and hydrolysis. In the oligosaccharide-free and cellobiose-bound CtCel9QΔc structures, a Tris molecule was found to be bound to three catalytic residues of CtCel9Q and occupied subsite -1 of the CtCel9Q active-site cleft. Moreover, the enzyme activity assay in the presence of 100 mm Tris showed that the Tris almost completely suppressed CtCel9Q hydrolase activity.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Sec 2, Taipei, 115, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GlucanaseA, B610Acetivibrio thermocellusMutation(s): 1 
Gene Names: celQ
EC: 3.2.1
UniProt
Find proteins for Q9AJF8 (Hungateiclostridium thermocellum)
Explore Q9AJF8 
Go to UniProtKB:  Q9AJF8
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-glucopyranose-(1-4)-beta-D-glucopyranoseC, E3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G14338VK
GlyCosmos:  G14338VK
GlyGen:  G14338VK
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranoseD, F2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G84824ZO
GlyCosmos:  G84824ZO
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7PE
Query on 7PE

Download Ideal Coordinates CCD File 
W [auth B]2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
C14 H30 O7
UKXKPKBTMYNOFS-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
M [auth A], N [auth A], O [auth A], R [auth B], U [auth B], V [auth B]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], P [auth B], Q [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], L [auth A], S [auth B], T [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900021
Query on PRD_900021
C, Ebeta-cellotrioseOligosaccharide /  Metabolism Ligand Interaction
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900005
Query on PRD_900005
D, Fbeta-cellobioseOligosaccharide /  Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.045α = 90
b = 108.668β = 90
c = 139.625γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology of TaiwanTaiwanNSC 102-2311-B-006-006-MY3
Ministry of Science and Technology of TaiwanTaiwanNSC 99-3113-B-001-001
Ministry of Science and Technology of TaiwanTaiwanMOST105-0210-01-12-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary