A new family of β-helix proteins with similarities to the polysaccharide lyases
Abstract
Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presented and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. More importantly, these results demonstrate how functional annotation by biochemicalmore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- New Mexico Consortium, Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1255244
- Report Number(s):
- LA-UR-15-26301
Journal ID: ISSN 1399-0047; ABCRE6; PII: S1399004714015934
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Acta Crystallographica. Section D: Biological Crystallography (Online)
- Additional Journal Information:
- Journal Name: Acta Crystallographica. Section D: Biological Crystallography (Online); Journal Volume: 70; Journal Issue: 10; Journal ID: ISSN 1399-0047
- Publisher:
- International Union of Crystallography
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; β-helix; polysaccharide lyase; gadolinium; functional annotation; Clostridium thermocellum; biomass degradation; cellulose; pectin; pectate; domain of unknown function; phage display; genome filtering
Citation Formats
Close, Devin W., D'Angelo, Sara, and Bradbury, Andrew R. M. A new family of β-helix proteins with similarities to the polysaccharide lyases. United States: N. p., 2014.
Web. doi:10.1107/S1399004714015934.
Close, Devin W., D'Angelo, Sara, & Bradbury, Andrew R. M. A new family of β-helix proteins with similarities to the polysaccharide lyases. United States. https://doi.org/10.1107/S1399004714015934
Close, Devin W., D'Angelo, Sara, and Bradbury, Andrew R. M. Sat .
"A new family of β-helix proteins with similarities to the polysaccharide lyases". United States. https://doi.org/10.1107/S1399004714015934. https://www.osti.gov/servlets/purl/1255244.
@article{osti_1255244,
title = {A new family of β-helix proteins with similarities to the polysaccharide lyases},
author = {Close, Devin W. and D'Angelo, Sara and Bradbury, Andrew R. M.},
abstractNote = {Microorganisms that degrade biomass produce diverse assortments of carbohydrate-active enzymes and binding modules. Despite tremendous advances in the genomic sequencing of these organisms, many genes do not have an ascribed function owing to low sequence identity to genes that have been annotated. Consequently, biochemical and structural characterization of genes with unknown function is required to complement the rapidly growing pool of genomic sequencing data. A protein with previously unknown function (Cthe_2159) was recently isolated in a genome-wide screen using phage display to identify cellulose-binding protein domains from the biomass-degrading bacterium Clostridium thermocellum. Here, the crystal structure of Cthe_2159 is presented and it is shown that it is a unique right-handed parallel β-helix protein. Despite very low sequence identity to known β-helix or carbohydrate-active proteins, Cthe_2159 displays structural features that are very similar to those of polysaccharide lyase (PL) families 1, 3, 6 and 9. Cthe_2159 is conserved across bacteria and some archaea and is a member of the domain of unknown function family DUF4353. This suggests that Cthe_2159 is the first representative of a previously unknown family of cellulose and/or acid-sugar binding β-helix proteins that share structural similarities with PLs. More importantly, these results demonstrate how functional annotation by biochemical and structural analysis remains a critical tool in the characterization of new gene products.},
doi = {10.1107/S1399004714015934},
journal = {Acta Crystallographica. Section D: Biological Crystallography (Online)},
number = 10,
volume = 70,
place = {United States},
year = {Sat Sep 27 00:00:00 EDT 2014},
month = {Sat Sep 27 00:00:00 EDT 2014}
}
Search WorldCat to find libraries that may hold this journalWeb of Science
Works referencing / citing this record:
Crystal structure of the catalytic unit of GH 87-type α-1,3-glucanase Agl-KA from Bacillus circulans
journal, October 2019
- Yano, Shigekazu; Suyotha, Wasana; Oguro, Natsuki
- Scientific Reports, Vol. 9, Issue 1
Molecular Dating of the Emergence of Anaerobic Rumen Fungi and the Impact of Laterally Acquired Genes
journal, August 2019
- Wang, Yan; Youssef, Noha H.; Couger, Matthew Brian
- mSystems, Vol. 4, Issue 4