4U5K | pdb_00004u5k

Complex structure of mutant CtCel5E (E314A) with cellobiose

• PDB DOI: https://doi.org/10.2210/pdb4U5K/pdb

• Classification: HYDROLASE
• Organism(s): Acetivibrio thermocellus ATCC 27405
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-07-25 Released: 2015-01-14 
• Deposition Author(s): Guo, R.T., Huang, C.H., Wu, T.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.255 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 

Starting Model: experimental

Literature

Biochemical Characterization and Structural Analysis of a Bifunctional Cellulase/Xylanase from Clostridium thermocellum

Yuan, S.F., Wu, T.H., Lee, H.L., Hsieh, H.Y., Lin, W.L., Yang, B., Chang, C.K., Li, Q., Gao, J., Huang, C.H., Ho, M.C., Guo, R.T., Liang, P.H.

(2015) J Biological Chem 290: 5739-5748

• PubMed: 25575592 
• DOI: https://doi.org/10.1074/jbc.M114.604454
• Primary Citation Related Structures: 
  4U3A, 4U5I, 4U5K


• PubMed Abstract: 
  

  We expressed an active form of CtCel5E (a bifunctional cellulase/xylanase from Clostridium thermocellum), performed biochemical characterization, and determined its apo- and ligand-bound crystal structures. From the structures, Asn-93, His-168, His-169, Asn-208, Trp-347, and Asn-349 were shown to provide hydrogen-bonding/hydrophobic interactions with both ligands. Compared with the structures of TmCel5A, a bifunctional cellulase/mannanase homolog from Thermotoga maritima, a flexible loop region in CtCel5E is the key for discriminating substrates. Moreover, site-directed mutagenesis data confirmed that His-168 is essential for xylanase activity, and His-169 is more important for xylanase activity, whereas Asn-93, Asn-208, Tyr-270, Trp-347, and Asn-349 are critical for both activities. In contrast, F267A improves enzyme activities.

---

Organizational Affiliation: 
• the Institute of Biochemical Sciences, and.
the Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan and.
From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.
the Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
the Institute of Biochemical Sciences, and From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, [e-mail].
the Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China [e-mail].
the Institute of Biochemical Sciences, and From the Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan, [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.07 kDa 
• Atom Count: 5,575 
• Modeled Residue Count: 602 
• Deposited Residue Count: 806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase H	A, B	403	Acetivibrio thermocellus ATCC 27405	Mutation(s): 1  Gene Names: celH, Cthe_1472 EC: 3.2.1.4
UniProt
Find proteins for P16218 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore P16218  Go to UniProtKB:  P16218

Oligosaccharides

Help  

Entity ID: 2
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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
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: 2.65 Å
• R-Value Free:  0.255 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.937	α = 90
b = 74.937	β = 90
c = 254.893	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Guo, R.T., Huang, C.H., Wu, T.H.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 1.2: 2015-03-11
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary