Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.70 kDa 
• Atom Count: 3583 
• Modelled Residue Count: 363 
• Deposited Residue Count: 363 
• Unique protein chains: 1

1KWF

Atomic Resolution Structure of an Inverting Glycosidase in Complex with Substrate

• PDB DOI: 10.2210/pdb1KWF/pdb

• Classification: HYDROLASE
• Organism(s): Acetivibrio thermocellus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-01-29 Released: 2002-03-13 
• Deposition Author(s): Guerin, D.M.A., Lascombe, M.-B., Costabel, M., Souchon, H., Lamzin, V., Beguin, P., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.113 
• R-Value Observed: 0.094 

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

• PubMed: 11884144 
• DOI: 10.1006/jmbi.2001.5404
• Primary Citation of Related Structures:  
  1KWF


• 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 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.

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Related Citations: 

• 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

• Crystallization of a family 8 cellulase from Clostridium thermocellum
  Souchon, H., Beguin, P., Alzari, P.M.
  (1996) Proteins 25: 134

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase A	A	363	Acetivibrio thermocellus	Mutation(s): 1  Gene Names: celA EC: 3.2.1.4
UniProt
Find proteins for A3DC29 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DC29  Go to UniProtKB:  A3DC29

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G91683DU GlyCosmos:  G91683DU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	C [auth A], D [auth A], E [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900016	B	beta-cellopentaose	Oligosaccharide / Metabolism		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.113 
• R-Value Observed: 0.094 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.336	α = 90
b = 62.767	β = 90
c = 103.493	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-29 
• Released Date: 2002-03-13 
Deposition Author(s): Guerin, D.M.A., Lascombe, M.-B., Costabel, M., Souchon, H., Lamzin, V., Beguin, P., Alzari, P.M.

Revision History  

• Version 1.0: 2002-03-13
  Type: Initial release
  
• Version 1.1: 2008-01-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-27
  Changes: Database references, Structure summary