5A8C

The ultra high resolution structure of a novel alpha-L-arabinofuranosidase (CtGH43) from Clostridium thermocellum ATCC 27405 with bound trimethyl N-Oxide (TRS)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.103 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16.

Goyal, A.Ahmed, S.Sharma, K.Gupta, V.Bule, P.Alves, V.D.Fontes, C.M.Najmudin, S.

(2016) Acta Crystallogr D Struct Biol 72: 1281-1289

  • DOI: 10.1107/S205979831601737X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degradin ...

    The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degrading enzymes. α-L-Arabinofuranosidases (EC 3.2.1.55) remove arabinose side chains from heteropolysaccharides such as xylan and arabinan. However, there is some evidence suggesting that arabinofuranosidases are substrate-specific, being unable to display a debranching activity on different polysaccharides. Here, the structure of Clostridium thermocellum arabinofuranosidase 43A (CtAbf43A), which has been shown to act in the removal of arabinose side chains from arabinoxylan but not from pectic arabinan, is reported. CtAbf43A belongs to GH43 subfamily 16, the members of which have a restricted capacity to attack xylans. The crystal structure of CtAbf43A comprises a five-bladed β-propeller fold typical of GH43 enzymes. CtAbf43A displays a highly compact architecture compatible with its high thermostability. Analysis of CtAbf43A along with the other member of GH43 subfamily 16 with known structure, the Bacillus subtilis arabinofuranosidase BsAXH-m2,3, suggests that the specificity of subfamily 16 for arabinoxylan is conferred by a long surface substrate-binding cleft that is complementary to the xylan backbone. The lack of a curved-shaped carbohydrate-interacting platform precludes GH43 subfamily 16 enzymes from interacting with the nonlinear arabinan scaffold and therefore from deconstructing this polysaccharide.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Crystallographic Analysis of a Novel Alpha-L-Arabinofuranosidase (Ctgh43) Fr Clostridium Thermocellum Atcc 27405.
      Goyal, A.,Ahmed, S.,Fontes, C.M.G.A.,Najmudin, S.
      (2014) Acta Crystallogr.,Sect.F 70: 616


    Organizational Affiliation

    Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBOHYDRATE BINDING FAMILY 6
A
326Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 0 
Find proteins for A3DEX4 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DEX4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.124 
  • R-Value Work: 0.103 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.440α = 90.00
b = 67.700β = 113.09
c = 51.010γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
BALBESphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Database references
  • Version 1.2: 2017-03-01
    Type: Database references