2ZZJ

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.

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)

wwPDB Validation 3D Report Full Report

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

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 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2009.03.034
Primary Citation of 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'.

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.

Macromolecule Content

Total Structure Weight: 27.57 kDa
Atom Count: 2,266
Modelled Residue Count: 238
Deposited Residue Count: 238
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6F143
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

Revision History (Full details and data files)

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