1GPI

Cellobiohydrolase Cel7D (CBH 58) from Phanerochaete chrysosporium. Catalytic module at 1.32 Angstrom resolution

PDB DOI: 10.2210/pdb1GPI/pdb

Classification: HYDROLASE
Organism(s): Phanerodontia chrysosporium
Mutation(s): No

Deposited: 2001-11-05 Released: 2002-01-01
Deposition Author(s): Munoz, I.G., Mowbray, S.L., Stahlberg, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.242
R-Value Work: 0.213
R-Value Observed: 0.216

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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Family 7 Cellobiohydrolases from Phanerochaete Chrysosporium: Crystal Structure of the Catalytic Module of Cel7D (Cbh58) at 1.32 Angstrom Resolution and Homology Models of the Isozymes.

Munoz, I.G., Ubhayasekera, W., Henriksson, H., Szabo, I., Pettersson, G., Johansson, G., Mowbray, S.L., Stahlberg, J.

(2001) J Mol Biol 314: 1097

PubMed: 11743726 Search on PubMed
DOI: 10.1006/jmbi.2000.5180
Primary Citation of Related Structures:
1GPI

PubMed Abstract:

Cellobiohydrolase 58 (Cel7D) is the major cellulase produced by the white-rot fungus Phanerochaete chrysosporium, constituting approximately 10 % of the total secreted protein in liquid culture on cellulose. The enzyme is classified into family 7 of the glycosyl hydrolases, together with cellobiohydrolase I (Cel7A) and endoglucanase I (Cel7B) from Trichoderma reesei. Like those enzymes, it catalyses cellulose hydrolysis with net retention of the anomeric carbon configuration. The structure of the catalytic module (431 residues) of Cel7D was determined at 3.0 A resolution using the structure of Cel7A from T. reesei as a search model in molecular replacement, and ultimately refined at 1.32 A resolution. The core structure is a beta-sandwich composed of two large and mainly antiparallel beta-sheets packed onto each other. A long cellulose-binding groove is formed by loops on one face of the sandwich. The catalytic residues are conserved and the mechanism is expected to be the same as for other family members. The Phanerochaete Cel7D binding site is more open than that of the T. reesei cellobiohydrolase, as a result of deletions and other changes in the loop regions, which may explain observed differences in catalytic properties. The binding site is not, however, as open as the groove of the corresponding endoglucanase. A tyrosine residue at the entrance of the tunnel may be part of an additional subsite not present in the T. reesei cellobiohydrolase. The Cel7D structure was used to model the products of the five other family 7 genes found in P. chrysosporium. The results suggest that at least two of these will have differences in specificity and possibly catalytic mechanism, thus offering some explanation for the presence of Cel7 isozymes in this species, which are differentially expressed in response to various growth conditions.

Organizational Affiliation:

Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Centre, SE-751 24 Uppsala, Sweden.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOGLUCANASE I	A	431	Phanerodontia chrysosporium	Mutation(s): 0 EC: 3.2.1.91 (PDB Primary Data), 3.2.1 (UniProt)
UniProt
Find proteins for Q7LIJ0 (Phanerodontia chrysosporium) Explore Q7LIJ0 Go to UniProtKB: Q7LIJ0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7LIJ0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 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		Ligand Interaction

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.242
R-Value Work: 0.213
R-Value Observed: 0.216
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.307	α = 90
b = 46.625	β = 103.19
c = 99.079	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2001-11-05
Released Date: 2002-01-01

Deposition Author(s):

Munoz, I.G.

Mowbray, S.L.

Stahlberg, J.

Revision History (Full details and data files)

Version 1.0: 2002-01-01
Type: Initial release
Version 1.1: 2011-09-07
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2017-03-29
Changes: Structure summary
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations
Version 2.0: 2020-03-11
Changes: Data collection, Other, Polymer sequence
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary