2ZZJ | pdb_00002zzj

Crystal structure of endo-beta-1,4-glucuronan lyase from fungus Trichoderma reesei

• PDB DOI: https://doi.org/10.2210/pdb2ZZJ/pdb

• Classification: LYASE
• Organism(s): Trichoderma reesei
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2009-02-16 Released: 2009-05-05 
• Deposition Author(s): Konno, N., Ishida, T., Fushinobu, S., Igarashi, K., Habu, N., Samejima, M., Isogai, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of polysaccharide lyase family 20 endo-beta-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei.

Konno, N., Ishida, T., Igarashi, K., Fushinobu, S., Habu, N., Samejima, M., Isogai, A.

(2009) FEBS Lett 583: 1323-1326

• PubMed: 19306878 
• DOI: https://doi.org/10.1016/j.febslet.2009.03.034
• Primary Citation Related Structures: 
  2ZZJ


• PubMed Abstract: 
  

  The crystal structure of endo-beta-(1-->4)-glucuronan lyase from Trichoderma reesei (TrGL) has been determined at 1.8A resolution as the first three-dimensional structure of polysaccharide lyase (PL) family 20. TrGL has a typical beta-jelly roll fold, which is similar to glycoside hydrolase family 16 and PL7 enzymes. A calcium ion is bound to the site far from the cleft and appears to contribute to the stability. There are several completely conserved residues in the cleft. Possible catalytic residues are predicted based on structural comparison with PL7 alginate lyase A1-II'.

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Organizational Affiliation: 
• Department of Biomaterials, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

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: 27.57 kDa 
• Atom Count: 2,266 
• Modeled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucuronan lyase A	A	238	Trichoderma reesei	Mutation(s): 0  Gene Names: glA EC: 4.2.2.14
UniProt
Find proteins for B6F143 (Hypocrea jecorina) Explore B6F143  Go to UniProtKB:  B6F143

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.287	α = 90
b = 62.301	β = 90
c = 129.121	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Konno, N., Ishida, T., Fushinobu, S., Igarashi, K., Habu, N., Samejima, M., Isogai, A.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary