3AMP

E134C-Cellotetraose complex of cellulase 12A from thermotoga maritima


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure and substrate-binding mode of cellulase 12A from Thermotoga maritima

Cheng, Y.-S.Ko, T.-P.Wu, T.-H.Ma, Y.Huang, C.-H.Lai, H.-L.Wang, A.H.-J.Liu, J.-R.Guo, R.-T.

(2011) Proteins 79: 1193-1204

  • DOI: 10.1002/prot.22953
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cellulases have been used in many applications to treat various carbohydrate-containing materials. Thermotoga maritima cellulase 12A (TmCel12A) belongs to the GH12 family of glycoside hydrolases. It is a β-1,4-endoglucanase that degrades cellulose mo ...

    Cellulases have been used in many applications to treat various carbohydrate-containing materials. Thermotoga maritima cellulase 12A (TmCel12A) belongs to the GH12 family of glycoside hydrolases. It is a β-1,4-endoglucanase that degrades cellulose molecules into smaller fragments, facilitating further utilization of the carbohydrate. Because of its hyperthermophilic nature, the enzyme is especially suitable for industrial applications. Here the crystal structure of TmCel12A was determined by using an active-site mutant E134C and its mercury-containing derivatives. It adopts a β-jellyroll protein fold typical of the GH12-family enzymes, with two curved β-sheets A and B and a central active-site cleft. Structural comparison with other GH12 enzymes shows significant differences, as found in two longer and highly twisted β-strands B8 and B9 and several loops. A unique Loop A3-B3 that contains Arg60 and Tyr61 stabilizes the substrate by hydrogen bonding and stacking, as observed in the complex crystals with cellotetraose and cellobiose. The high-resolution structures allow clear elucidation of the network of interactions between the enzyme and its substrate. The sugar residues bound to the enzyme appear to be more ordered in the -2 and -1 subsites than in the +1, +2 and -3 subsites. In the E134C crystals the bound -1 sugar at the cleavage site consistently show the α-anomeric configuration, implicating an intermediate-like structure.


    Organizational Affiliation

    Institute of Biotechnology, National Taiwan University, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-1,4-beta-glucanase
A, B
265Thermotoga maritimaMutation(s): 1 
Gene Names: celA
EC: 3.2.1.4
Find proteins for Q60032 (Thermotoga maritima)
Go to UniProtKB:  Q60032
Small Molecules
Ligands 2 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
CTR
Query on CTR

Download SDF File 
Download CCD File 
A, B
CELLOTRIOSE
Dextrin
C18 H32 O16
FYGDTMLNYKFZSV-RZDZXANRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.076α = 90.00
b = 73.906β = 90.00
c = 179.664γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
Blu-Icedata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-01-29
    Type: Database references
  • Version 1.3: 2017-10-11
    Type: Refinement description