1KWF

Atomic Resolution Structure of an Inverting Glycosidase in Complex with Substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.113 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate.

Guerin, D.M.Lascombe, M.B.Costabel, M.Souchon, H.Lamzin, V.Beguin, P.Alzari, P.M.

(2002) J.Mol.Biol. 316: 1061-1069

  • DOI: 10.1006/jmbi.2001.5404

  • PubMed Abstract: 
  • The crystal structure of Clostridium thermocellum endoglucanase CelA in complex with cellopentaose has been determined at 0.94 A resolution. The oligosaccharide occupies six D-glucosyl-binding subsites, three on either side of the scissile glycosidic ...

    The crystal structure of Clostridium thermocellum endoglucanase CelA in complex with cellopentaose has been determined at 0.94 A resolution. The oligosaccharide occupies six D-glucosyl-binding subsites, three on either side of the scissile glycosidic linkage. The substrate and product of the reaction occupy different positions at the reducing end of the cleft, where an extended array of hydrogen-bonding interactions with water molecules fosters the departure of the leaving group. Severe torsional strain upon the bound substrate forces a distorted boat(2,5) B conformation for the glucosyl residue bound at subsite -1, which facilitates the formation of an oxocarbenium ion intermediate and might favor the breakage of the sugar ring concomitant with catalysis.


    Related Citations: 
    • Crystallization of a family 8 cellulase from Clostridium thermocellum
      Souchon, H.,Beguin, P.,Alzari, P.M.
      (1996) PROTEINS: STRUCT.,FUNCT.,GENET. 25: 134
    • The crystal structure of endoglucanase CelA, a family 8 glycosyl hydrolase from Clostridium thermocellum.
      Alzari, P.M.,Souchon, H.,Dominguez, R.
      (1996) Structure 4: 265


    Organizational Affiliation

    Unité de Biochimie Structurale, CNRS URA 2185, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris cédex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endoglucanase A
A
363Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)Mutation(s): 1 
Gene Names: celA
EC: 3.2.1.4
Find proteins for A3DC29 (Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Go to UniProtKB:  A3DC29
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.113 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.336α = 90.00
b = 62.767β = 90.00
c = 103.493γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SHELXL-97refinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-01-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance