3II1

Structural characterization of difunctional glucanase-xylanse CelM2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of the bifunctional glucanase-xylanase CelM2 reveals the metal effect and substrate-binding moiety

Nam, K.H.Lee, W.H.Rhee, K.H.Hwang, K.Y.

(2010) Biochem Biophys Res Commun 391: 1726-1730

  • DOI: 10.1016/j.bbrc.2009.12.141
  • Primary Citation of Related Structures:  
    3II1

  • PubMed Abstract: 
  • The bifunctional glycoside hydrolase enzyme, CelM2, is able to hydrolyze glucan and xylan effectively. The crystal structure of this protein has been determined, providing useful sequential and structural information [K.H. Nam, S.J. Kim, K.Y. Hwang, Crystal structure of CelM2, a bifunctional glucanase-xylanase protein from a metagenome library, Biochem ...

    The bifunctional glycoside hydrolase enzyme, CelM2, is able to hydrolyze glucan and xylan effectively. The crystal structure of this protein has been determined, providing useful sequential and structural information [K.H. Nam, S.J. Kim, K.Y. Hwang, Crystal structure of CelM2, a bifunctional glucanase-xylanase protein from a metagenome library, Biochem. Biophys. Res. Commun. 383 (2009) 183-186]. In addition, this protein is a good model for understanding bifunctional enzymes, and it will provide information relevant for genetic engineering that will be useful in the design of bifunctional proteins. However, previous structural characterization was not sufficient to develop an understanding of the metal ion and substrate-binding moiety. Herein, we determined the metal-binding site of CelM2 using zinc ions. Our results revealed that the zinc ions participate in the crystallographic packing and enzyme folding of the external region of the TIM-like barrel domain. Based on our structure, zinc ions induce the passive form of the CAP region at the catalytic cleft of the CelM2 protein. Moreover, glucose was bound to the CelM2 structure at the catalytic site. This structure provides the binding moiety that binds to the hydroxyl group of substrates such as cellulose. In addition, a structural comparison of celM2 with Cel44 provides a good model of the binding mode of CelM2. Thus, our study represents a novel structural characterization of the metal-binding site and the structure of the complex formed between CelM2 and its substrate.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul 136-701, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CellulaseA535uncultured bacteriumMutation(s): 0 
Gene Names: celM2
EC: 3.2.1.4
UniProt
Find proteins for A1E9A6 (uncultured bacterium)
Explore A1E9A6 
Go to UniProtKB:  A1E9A6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
B [auth A]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.594α = 90
b = 87.431β = 90
c = 110.574γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2009-07-31 
  • Released Date: 2009-08-25 
  • Deposition Author(s): Hwang, K.Y., Nam, K.H.

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary