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An analysis of
pdb-care (PDB CArbohydrate REsidue check): a
program to support annotation of complex
carbohydrate structures in PDB files
by Thomas Lütteke
and Claus-W von der Lieth
By David Chapman
Background
Protein Data Bank includes 3-D data for
carbohydrate structures as well as amino acid
structures
3-D data for protein / carbohydrate interactions is
analyzed through X-Ray crytallography and
Nuclear Magnetic Resonance
The absence of 3-D glycan data in PDB does
not necessarily mean a potential glycosolation
site is unoccupied
Background
The crytallography may have been done on
plasmid replicated proteins, which may not
have the same carbohydrates attached as the
human form.
Glycosylation usually occurs at asparagine
residues in Asn-X-Ser/Thr sequons where X
does not equal proline
Approximately 30% of all 1663 PDB entries
(Sep 2003) containing carbohydrates contain
errors in glycan description
Biological Significance
Protein / Carbohydrate interactions are
important because they are involved in a
variety of biological processes
Fertilization
Embryonic development
Cellular differentiation
Background
High error rate in PDB glycan description is mainly due to
incorrect assignment of saccharide units
Sequences for complex carbohydrates differ
significantly from single letter amino acid sequences
The number of naturally occurring residues is much
larger for carbohydrates
Each pair of monosaccharide residues can be linked in
several ways
A residue can be connected to three or four others
(branching)
Background
Unlike amino acids, carbohydrates use a
three letter code which are defined the HET
dictionary in PDB
A new residue name is required for each
stereochemically different sugar unit
This makes the correct assignment
complicated, tedious and error prone
Background
Examples of Definitions of carbohydrate
residues:
AGC
alpha-D-Glucopyranose
BGC
beta -D-Glucopyranose
FCA
alpha-D-Fucose
FCB
beta-D-Fucose
There are more than 200 carbohydrate residues
used in PDB
Implementation
Pdb-care is based on the pdb2linucs carbohydrate detection
program
Pdb2linucs is able to identify and assign carbohydrate
structures using only the reported atom types and their
3D coordinates
The program output is in LINUCS notation and is used
to normalize complex carbohydrate structures
Pdb-care uses a translation table built in XML in order to
compare the LINUCS notation from pdb2linucs to the
residue assignments in the PDB group dictionary
Implementation
The translation table contains:
141 monosaccharides
31 oligosaccharides
77 combined residues
Pdb-care was written in the C language
Front end is a web interface implemented in
PHP
Implementation
Pdb-care web interface can accommodate
either direct input using copy/paste of a pdb
file or locating a file on a local hard drive or
using a PDB-ID
The pdb-care protocol reports the type of
problems, inconsistencies and errors
detected
Program Example
pdb-care examples
Conclusion
The authors made relevant points regarding the
biological significance of protein-carbohydrate
interactions and the need for accurate glycan
residue information in PDB.
However, the authors did not go into detail
regarding the actual implementation of the
translation table used in pdb-care so it is difficult
to judge the accuracy of their program.