7NDE

Trichoderma parareesei PL7A beta-glucuronan lyase

• PDB DOI: https://doi.org/10.2210/pdb7NDE/pdb

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


• Deposited: 2021-02-01 Released: 2022-03-02 
• Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Glucuronan lyases from family PL7 use a Tyr/Tyr syn beta-elimination catalytic mechanism for glucuronan breakdown.

Vuillemin, M., Pilgaard, B., Kiehn, E., Fredslund, F., Welner, D.H., Meyer, A.S., Aachmann, F.L., Wilkens, C.

(2024) Chem Commun (Camb) 60: 440-443

• PubMed: 38087900 
• DOI: https://doi.org/10.1039/d3cc04256a
• Primary Citation of Related Structures:  
  7NDE


• PubMed Abstract: 
  

  TpPL7A and TpPL7B, members of CAZy family PL7, act as β-glucuronan lyases. TpPL7A diverges by lacking the catalytic histidine, identified as the Brønsted base in PL7 alginate lyases. Our research, including TpPL7A's crystal structure, and mutagenesis studies, reveals a shared syn -β-elimination mechanism with a single tyrosine serving as both base and acid catalyst. This mechanism may extend to subfamily PL7_4 glucuronan lyases.

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Organizational Affiliation: 

Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26 kDa 
• Atom Count: 2,041 
• Modelled Residue Count: 233 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucuronan lyase	A	242	Trichoderma parareesei	Mutation(s): 0  Gene Names: A9Z42_0012760
UniProt
Find proteins for A0A2H2ZFD4 (Trichoderma parareesei) Explore A0A2H2ZFD4  Go to UniProtKB:  A0A2H2ZFD4
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.174 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.589	α = 90
b = 69.589	β = 90
c = 111.66	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing
PHENIX	refinement
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Fredslund, F., Welner, D.H., Wilkens, C.

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-02-14
  Changes: Database references
• Version 1.3: 2024-10-16
  Changes: Structure summary