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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.174
R-Value Work: 0.155
R-Value Observed: 0.156

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kgs. Lyngby, Denmark. cpwk@novonordisk.com.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2H2ZFD4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]