On the other hand

Mirror imageThe vast majority of amino acid residues that appear in peptides and proteins appear as their natural L-form enantiomer. This is the form of all amino acids as translated by the ribosome. However post-translational modification, such as by racemases, or peptide synthetic methods can be used to introduce the mirror image D-forms of amino acids into peptidic compounds.

Though rare, it is often important to keep track of whether individual amino acids are L-form, D-form, unknown or a racemic mixture of the two (DL-form). Rather unhelpfully, IUPAC rule 3AA-3.3 from IUPAC’s “Nomenclature and Symbolism for amino acids and peptides” states that the configuration prefix may be omitted for amino acids from a natural protein source (where the configuration may be assumed to be L) and for amino acids from synthetic sources (where the configuration is assumed to be an equimolecular mixture of enantiomers).

In the RCSB’s PDB file format, three letter residue codes have been assigned for both the L- form and the D- form of the traditional 19 amino acids other than glycine. Glycine (PDB residue code GLY) has an achiral α-carbon and therefore does not have an L-form and a D-form. For convenience, the table below lists the correspondence between PDB’s three letter codes for these amino acids.

Name L-form D-form
Alanine ALA DAL
Arginine ARG DAR
Asparagine ASN DSG
Aspartic Acid ASP DAS
Cysteine CYS DCY
Glutamine GLN DGN
Glutamic Acid GLU DGL
Histidine HIS DHI
Isoleucine ILE DIL
Leucine LEU DLE
Lysine LYS DLY
Methionine MET MED
Phenylalanine PHE DPN
Proline PRO DPR
Serine SER DSN
Threonine THR DTH
Tryptophan TRP DTR
Tyrosine TYR DTY
Valine VAL DVA

The above table is believed to be the only internet resource conveniently linking the two PDB residue codes for enantiomeric forms of amino acids.

Unfortunately for the two recent natural amino acids, selenocysteine (PDB residue code CSE) and pyrrolysine (PDB residue code PYH), no PDB residue codes have yet been assigned for their enantiomeric D-forms.

Image credit: The Joneses (where are the joneses on Flickr)

2 thoughts on “On the other hand”

  1. an additional note to the problem with the amino acids and the configuration: the recommended name of l-lysine is according WHO INN lysine (r-list 28, Vol2, Nr3, 1988), without any stereo descriptor.

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