Binding sub-site dissection of a carbohydrate-binding module reveals the contribution of entropy to oligosaccharide recognition at "non-primary" binding subsites

Journal of Molecular Biology
Alicia Lammerts van Bueren, Alisdair B Boraston

Abstract

The optimal ligands for many carbohydrate-binding proteins are often oligosaccharides comprising two, three, or more monosaccharide units. The binding affinity for these sugars is increased incrementally by contributions from binding subsites on the protein that accommodate the individual monosaccharide residues of the oligosaccharide. Here, we use CsCBM6-1, a xylan-specific type B carbohydrate-binding module (CBM) from Clostridium stercorarium falling into amino acid sequence family CBM6, as a model system to investigate the structural and thermodynamic contributions of binding subsites in this protein to carbohydrate recognition. The three-dimensional structures of uncomplexed CsCBM6-1 (at 1.8 A resolution) and bound to the oligosaccharides xylobiose, xylotriose, and xylotetraose (at 1.70 A, 1.89 A, and 1.69 A resolution, respectively) revealed the sequential occupation of four subsites within the binding site in the order of subsites 2, 3, 4 then 1. Overall, binding to all of the xylooligosaccharides tested was enthalpically favourable and entropically unfavourable, like most protein-carbohydrate interactions, with the primary subsites 2 and 3 providing the bulk of the free energy and enthalpy of binding. In contrast, the co...Continue Reading

References

Jun 11, 1992·Protein Engineering·J M GreenwoodD G Kilburn
May 25, 1999·Protein Science : a Publication of the Protein Society·E García-Hernández, A Hernández-Arana
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·G CarrardP Béguin
Nov 28, 2000·Acta Crystallographica. Section D, Biological Crystallography·A Vagin, A Teplyakov
Apr 3, 2001·Protein Expression and Purification·A B BorastonD G Kilburn
Dec 18, 2001·The Biochemical Journal·Alisdair B BorastonDouglas G Kilburn
Feb 19, 2002·Molecular Microbiology·Alisdair B BorastonDouglas G Kilburn
Jun 25, 2002·Journal of Molecular Biology·Alisdair B BorastonGideon J Davies
Nov 13, 2002·The Journal of Biological Chemistry·Alisdair B BorastonDouglas G Kilburn
Dec 21, 2002·Protein Science : a Publication of the Protein Society·Enrique García-HernándezMiguel Costas
Dec 4, 2003·Journal of the American Chemical Society·W Bruce Turnbull, Antonio H Daranas
Feb 18, 2004·Current Protein & Peptide Science·Ilan Levy, Oded Shoseyov
Mar 9, 2004·The Journal of Biological Chemistry·Joanna L HenshawHarry J Gilbert
Sep 1, 1994·Acta Crystallographica. Section D, Biological Crystallography·UNKNOWN Collaborative Computational Project, Number 4
May 1, 1997·Acta Crystallographica. Section D, Biological Crystallography·G N MurshudovE J Dodson

❮ Previous
Next ❯

Citations

Aug 29, 2006·Analytical Biochemistry·Henrik A EngströmSten Ohlson
Jan 12, 2017·Chembiochem : a European Journal of Chemical Biology·Giulio NavarraBeat Ernst
May 27, 2017·Proteins·Silvia ArmentaRomina Rodríguez-Sanoja
Oct 27, 2004·The Journal of Biological Chemistry·Alicia Lammerts van BuerenAlisdair B Boraston
Feb 23, 2008·The Journal of Biological Chemistry·Katie J GreggAlisdair B Boraston
Sep 23, 2006·The Journal of Biological Chemistry·Elizabeth Ficko-Blean, Alisdair B Boraston
May 4, 2005·The Journal of Biological Chemistry·Hitomi IchinoseSatoshi Kaneko
Mar 6, 2021·Scientific Reports·Joni VuorioHector Martinez-Seara

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.