4XWM | pdb_00004xwm

Complex structure of catalytic domain of Clostridium Cellulovorans Exgs and Cellobiose

• PDB DOI: https://doi.org/10.2210/pdb4XWM/pdb
• Entry: 4XWM supersedes: 4KKF

• Classification: HYDROLASE
• Organism(s): Clostridium cellulovorans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-29 Released: 2015-10-28 
• Deposition Author(s): Liaw, Y.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.163 (Depositor), 0.165 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Structures of exoglucanase from Clostridium cellulovorans: cellotetraose binding and cleavage

Tsai, L.-C., Amiraslanov, I., Chen, H.R., Chen, Y.W., Lee, H.L., Liang, P.H., Liaw, Y.-C.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1264-1272

• PubMed: 26457517 
• DOI: https://doi.org/10.1107/S2053230X15015915
• Primary Citation Related Structures: 
  4XWL, 4XWM, 4XWN


• PubMed Abstract: 
  

  Exoglucanase/cellobiohydrolase (EC 3.2.1.176) hydrolyzes a β-1,4-glycosidic bond from the reducing end of cellulose and releases cellobiose as the major product. Three complex crystal structures of the glycosyl hydrolase 48 (GH48) cellobiohydrolase S (ExgS) from Clostridium cellulovorans with cellobiose, cellotetraose and triethylene glycol molecules were solved. The product cellobiose occupies subsites +1 and +2 in the open active-site cleft of the enzyme-cellotetraose complex structure, indicating an enzymatic hydrolysis function. Moreover, three triethylene glycol molecules and one pentaethylene glycol molecule are located at active-site subsites -2 to -6 in the structure of the ExgS-triethylene glycol complex shown here. Modelling of glucose into subsite -1 in the active site of the ExgS-cellobiose structure revealed that Glu50 acts as a proton donor and Asp222 plays a nucleophilic role.

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Organizational Affiliation: 
• Molecular Science and Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao E. Road, Taipei 10608, Taiwan.
Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan.
Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Taipei 11529, Taiwan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 77.06 kDa 
• Atom Count: 5,828 
• Modeled Residue Count: 630 
• Deposited Residue Count: 681 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exoglucanase S	A	681	Clostridium cellulovorans	Mutation(s): 0  Gene Names: exgS EC: 3.2.1.91
UniProt
Find proteins for O65986 (Clostridium cellulovorans) Explore O65986  Go to UniProtKB:  O65986

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G86802XL GlyCosmos: G86802XL

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900023	B	alpha-cellobiose	Oligosaccharide / Metabolism

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	C, D	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.163 (Depositor), 0.165 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.14	α = 90
b = 109.14	β = 90
c = 182.145	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Liaw, Y.-C.
• This entry supersedes: 4KKF

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary