ProCarbDB: a database of carbohydrate-binding proteins.

Liviu Copoiu,Tom L Blundell,Pedro H M Torres,Sony Malhotra,David B Ascher

doi:10.1093/nar/gkz860

Liviu Copoiu, Tom L Blundell + Show 3 more

Open Access

https://doi.org/10.1093/nar/gkz860

Copy DOI

Abstract

Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein–carbohydrate interfaces. In order to better understand protein–carbohydrate interactions, we have developed an open-access database, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the complete carbohydrate ligands and their monomeric units. ProCarbDB is a comprehensive database containing over 5200 3D X-ray crystal structures of protein–carbohydrate complexes. In ProCarbDB, the complete carbohydrate ligands are annotated and all their interactions are displayed. Users can also select any protein residue in the proximity of the ligand to inspect its interactions with the carbohydrate ligand and with other neighbouring protein residues. Where available, additional curated information on the binding affinity of the complex and the effects of mutations on the binding have also been provided in the database. We believe that ProCarbDB will be an invaluable resource for understanding protein–carbohydrate interfaces. The ProCarbDB web server is freely available at http://www.procarbdb.science/procarb.

Highlights

Carbohydrates are amongst the most versatile classes of ligands, being able to form complex, branched glycans from monosaccharide units
We describe ProCarbDB, a freely accessible, user friendly database that comprises of 5242 true protein– carbohydrate complexes
(iv) Structures that contained only crystallographic adjuvants (e.g. B-octylglucoside) by using a semi-automatic text-mining algorithm based on cross-reference between well-established databases such as UniProt [29], Protein Data Bank (PDB) [7] and ENZYME database [30]

Summary

Introduction

Carbohydrates are amongst the most versatile classes of ligands, being able to form complex, branched glycans from monosaccharide units This generates a complex structural pattern, commonly referred to as the glycocode, which carbohydrate-binding proteins are able to decipher [1]. Identifying sugar moieties in the Protein Data Bank (PDB) [7] is challenging, as some of the carbohydrate entries are poorly annotated [8]. This is in part due to the large number of naturally occurring monosaccharides, and due to the multiple ways saccharide units may be linked and the complex branching capacity of polysaccharides

Objectives

Methods

Results

Conclusion