2EJ1 | pdb_00002ej1

Crystal structure of Cel44A, GH family 44 endoglucanase from Clostridium thermocellum

• PDB DOI: https://doi.org/10.2210/pdb2EJ1/pdb

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


• Deposited: 2007-03-14 Released: 2007-09-18 
• Deposition Author(s): Kitago, Y., Karita, S., Watanabe, N., Sakka, K., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.185 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellum.

Kitago, Y., Karita, S., Watanabe, N., Kamiya, M., Aizawa, T., Sakka, K., Tanaka, I.

(2007) J Biological Chem 282: 35703-35711

• PubMed: 17905739 
• DOI: https://doi.org/10.1074/jbc.M706835200
• Primary Citation Related Structures: 
  2E0P, 2E4T, 2EEX, 2EJ1, 2EO7, 2EQD


• PubMed Abstract: 
  

  The crystal structure of Cel44A, which is one of the enzymatic components of the cellulosome of Clostridium thermocellum, was solved at a resolution of 0.96 A. This enzyme belongs to glycoside hydrolase family (GH family) 44. The structure reveals that Cel44A consists of a TIM-like barrel domain and a beta-sandwich domain. The wild-type and the E186Q mutant structures complexed with substrates suggest that two glutamic acid residues, Glu(186) and Glu(359), are the active residues of the enzyme. Biochemical experiments were performed to confirm this idea. The structural features indicate that GH family 44 belongs to clan GH-A and that the reaction catalyzed by Cel44A is retaining type hydrolysis. The stereochemical course of hydrolysis was confirmed by a (1)H NMR experiment using the reduced cellooligosaccharide as a substrate.

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Organizational Affiliation: 
• Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 0600810, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 59 kDa 
• Atom Count: 4,746 
• Modeled Residue Count: 509 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A	519	Acetivibrio thermocellus	Mutation(s): 1  Gene Names: CelJ, CelJ-Cel9D-Cel44A EC: 3.2.1.4 (PDB Primary Data), 3.2.1.151 (PDB Primary Data)
UniProt
Find proteins for A3DD30 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DD30  Go to UniProtKB:  A3DD30

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan: G09454VW GlyCosmos: G09454VW GlyGen: G09454VW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020	B	beta-cellohexaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.185 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.898	α = 90
b = 59.095	β = 90
c = 171.33	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Kitago, Y., Karita, S., Watanabe, N., Sakka, K., Tanaka, I.

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary
• Version 2.2: 2023-10-25
  Changes: Data collection, Refinement description