Orientation of Alditol Residues
(also applies to aldaric acids, dialdoses, diketoses, etc.)
In standard aldose monosaccharides the backbone orientation is clearly defined by the aldehyde group, the carbon of which is denoted by "C1". If the aldehyde group is missing, however, finding the correct C1 is more complex. This is the case e.g. with alditols or aldaric acids. The same problem also applies to dialdoses, which have two aldehyde groups, both of which could mark the C1 atom. The rules to be followed are described in IUPAC Rules 2-Carb-2 and 2-Carb-11.
MonosaccharideDB implements these rules in its internal notation checks. This means that, depending on the residue name used to query the database, the resulting entry might have an inverse backbone orientation compared with the query name. For example, when querying the database using the CarbBank-style residue name L-Xyl-ol, you will be directed to the D-Xyl-ol entry.
These two residues are chemically identical and differ only in atom numbering resuling from a different choise of C1 atom (see figure on the left: atom numbers of L-Xyl-ol are indicated in blue, those of D-Xyl-ol in red). This leads to an inversion of monosaccharide backbone orientation implicating a rotation by 180°.
Implications on linkage notation
A warning message notifying this inversion of backbone orientation to the user is displayed on top of the entry when queried with a residue name that implies "wrong" orientation, such as the L-Xyl-ol query above. This change of backbone orientation has to be taken into account by the user, because the altered atom numbering might affect linking positions of residues that form a glycosidic linkage to the residue in question. Substituent positions are automatically updated by MonosaccharideDB, e.g. L-Xyl-ol-2Ac is renamed as D-Xyl-ol-4Ac. When the residue is part of an oligosaccharide and linked to other monosaccharides, however, the adaption of linking positions to residues that are not included in the query has to be done by the user when correcting the residue name within the oligosaccharide.
For example, the disaccharide b-D-Galp-(1-2)-L-Xyl-ol has to be corrected to b-D-Galp-(1-4)-D-Xyl-ol.