5XCY

Structure of the cellobiohydrolase Cel6A from Phanerochaete chrysosporium at 1.2 angstrom

PDB DOI: https://doi.org/10.2210/pdb5XCY/pdb

Classification: HYDROLASE
Organism(s): Phanerodontia chrysosporium
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2017-03-24 Released: 2017-07-26
Deposition Author(s): Tachioka, M., Nakamura, A., Ishida, T., Igarashi, K., Samejima, M.
Funding Organization(s): Japanese Ministry of Education, Culture, Sports, and Technology, Japan Society for the Promotion of Science

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.158
R-Value Work: 0.138
R-Value Observed: 0.139

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a family 6 cellobiohydrolase from the basidiomycete Phanerochaete chrysosporium

Tachioka, M., Nakamura, A., Ishida, T., Igarashi, K., Samejima, M.

(2017) Acta Crystallogr F Struct Biol Commun 73: 398-403

PubMed: 28695848 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X17008093
Primary Citation of Related Structures:
5XCY, 5XCZ

PubMed Abstract:
Cellobiohydrolases belonging to glycoside hydrolase family 6 (CBH II, Cel6A) play key roles in the hydrolysis of crystalline cellulose. CBH II from the white-rot fungus Phanerochaete chrysosporium (PcCel6A) consists of a catalytic domain (CD) and a carbohydrate-binding module connected by a linker peptide, like other known fungal cellobiohydrolases. In the present study, the CD of PcCel6A was crystallized without ligands, and p-nitrophenyl β-D-cellotrioside (pNPG3) was soaked into the crystals. The determined structures of the ligand-free and pNPG3-soaked crystals revealed that binding of cellobiose at substrate subsites +1 and +2 induces a conformational change of the N-terminal and C-terminal loops, switching the tunnel-shaped active site from the open to the closed form.

Organizational Affiliation

Department of Biomaterial Sciences, 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: 38.38 kDa
Atom Count: 3,520
Modelled Residue Count: 358
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucanase	A	358	Phanerodontia chrysosporium	Mutation(s): 0 Gene Names: cel6A EC: 3.2.1
UniProt
Find proteins for Q02321 (Phanerodontia chrysosporium) Explore Q02321 Go to UniProtKB: Q02321
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02321
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.158
R-Value Work: 0.138
R-Value Observed: 0.139
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.712	α = 90
b = 67.18	β = 90
c = 89.113	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2017-07-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Japanese Ministry of Education, Culture, Sports, and Technology	Japan	24114001
Japanese Ministry of Education, Culture, Sports, and Technology	Japan	24114008
Japan Society for the Promotion of Science	Japan	24380089
Japan Society for the Promotion of Science	Japan	15J10657