6IDW

GH6 Orpinomyces sp. Y102 enzyme

PDB DOI: https://doi.org/10.2210/pdb6IDW/pdb
Entry: 6IDW supersedes: 5JX6

Classification: HYDROLASE
Organism(s): Orpinomyces sp. Y102
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2018-09-11 Released: 2018-10-17
Deposition Author(s): Tsai, L.C., Huang, H.C.
Funding Organization(s): National Science Council (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.253
R-Value Work: 0.220
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structures of the GH6 Orpinomyces sp. Y102 CelC7 enzyme with exo and endo activity and its complex with cellobiose.

Huang, H.C., Qi, L.H., Chen, Y.C., Tsai, L.C.

(2019) Acta Crystallogr D Struct Biol 75: 1138-1147

PubMed: 31793907 Search on PubMed
DOI: https://doi.org/10.1107/S2059798319013597
Primary Citation of Related Structures:
6IDW

PubMed Abstract:
The catalytic domain (residues 128-449) of the Orpinomyces sp. Y102 CelC7 enzyme (Orp CelC7) exhibits cellobiohydrolase and cellotriohydrolase activities. Crystal structures of Orp CelC7 and its cellobiose-bound complex have been solved at resolutions of 1.80 and 2.78 Å, respectively. Cellobiose occupies subsites +1 and +2 within the active site of Orp CelC7 and forms hydrogen bonds to two key residues: Asp248 and Asp409. Furthermore, its substrate-binding sites have both tunnel-like and open-cleft conformations, suggesting that the glycoside hydrolase family 6 (GH6) Orp CelC7 enzyme may perform enzymatic hydrolysis in the same way as endoglucanases and cellobiohydrolases. LC-MS/MS analysis revealed cellobiose (major) and cellotriose (minor) to be the respective products of endo and exo activity of the GH6 Orp CelC7.

Organizational Affiliation

Institute of Organic and Polymeric Materials, National Taipei University of Technology, Taipei, Taiwan.

Macromolecule Content

Total Structure Weight: 143.95 kDa
Atom Count: 10,479
Modelled Residue Count: 1,288
Deposited Residue Count: 1,288
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, B, C, D	322	Orpinomyces sp. Y102	Mutation(s): 0 Gene Names: cbhC7 EC: 3.2.1
UniProt
Find proteins for A0A076U926 (Orpinomyces sp. Y102) Explore A0A076U926 Go to UniProtKB: A0A076U926
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A076U926
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	E, F, G, H	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C]	I [auth A], L [auth B], P [auth C], Q [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C]	K [auth A], M [auth B], O [auth B], R [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain R [auth C] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain R [auth C]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	E, F, G, H	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.78 Å
R-Value Free: 0.253
R-Value Work: 0.220
R-Value Observed: 0.221
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 310.369	α = 90
b = 86.594	β = 93.67
c = 82.314	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

Tsai, L.C.

Huang, H.C.

This entry supersedes: 5JX6

Funding Organization	Location	Grant Number
National Science Council (Taiwan)	Taiwan	NSC101-2311-B-027-001

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2019-10-30
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-22
Changes: Data collection, Database references, Refinement description, Structure summary