UniProt release 15.12
Published December 15, 2009
Through the Looking-Glass
All amino acids but glycine can exist in either of two optical isomers, called L-or D-amino acids, which are mirror images of each other. However, we have been taught for decades that proteins that occur in nature are made out of L-forms. There are some well-known exceptions, of course, but restricted to prokaryotes. Indeed, D-forms are abundant components of the peptidoglycan cell walls of bacteria, and are also observed in bacterial natural antibiotics, such as actinomycin D, bacitracin or tetracycline. These latter are quite unusual peptides that are synthesized by multienzyme complexes in a stepwise fashion without the participation of mRNA. It has also been observed that the mammalian brain contains high levels of free D-serine which appears to be a physiological coagonist of N-methyl D-aspartate receptors (NMDARs) and, as such, may act as a neurotransmitter in the brain, but this activity is carried out by the amino acid itself and does not occur within the context of a polypeptide. The isolation, in the 1980s, of naturally occurring animal peptides containing D-amino acids challenged the dogma, leading to the discovery of a new post-translational modification (PTM): L- to D-isomerization.
In 1981, Montecucchi et al., looking for enkephalin-related peptides in various amphibia, isolated dermorphin from the skin of Phyllomedusa sauvagei. Dermorphin is produced by 2 different precursors: cleavage of Dermorphin-1 gives rise to 4 mature dermorphins and that of Dermorphin-2 to 5 mature peptides, all of which have the identical sequence: YAFGYPS. This heptapeptide binds with high affinity and selectivity to mu-type opioid receptors and appears to be a thousand times more potent than morphine in inducing deep long-lasting analgesia when injected into mice or rats. Interestingly, the second amino acid of dermorphin is D-alanine. A synthetic isomer, containing L-alanine at that position, is virtually devoid of biological activity.
This discovery was followed by many others. Deltorphins, another class of frog opioid peptides, also characterized by a D-amino acid at position 2, were isolated. Another amphibian, Bombina variegata, was shown to express antimicrobial D-amino acid-containing peptides, called bombesins, on its skin. Arthropoda, such as spider, lobsters and crayfish, and Mollusca entered the game. Cone snail peptide toxins have been extensively studied in this context and they currently represent 60% of all animal D-amino acid-containing proteins annotated in UniProtKB/Swiss-Prot. A single mammal appears on the list: platypus with 2 peptides, C-type natriuretic peptide 39 and Defensin-like peptide 2/4, expressed in its venom gland.
Animal D-amino acid-containing proteins are synthesized on ribosomes following a classical mRNA template; unusual codons have not been observed. In addition, some of them have been isolated from their biological source with both L- and D-amino acid at the appropriate position. These observations suggested that L- to D-amino acid isomerization is a bona fide PTM. An enzyme catalyzing the conversion of an Omega-agatoxin-Aa4b serine (at position 46 of the mature peptide, 81 in the precursor) from L- to D-form has been isolated from the funnel-web spider Agelenopsis aperta and its partial sequence is available in UniProtKB/TrEMBL. A similar mammalian activity has been characterized from platypus venom.
L- to D-amino acid isomerization presents significant advantages. The modified peptides become more resistant to protease degradation and hence much more stable. In addition, X-ray crystallography studies have shown that the isomerization creates new structures, such as peculiar beta-turns. The creation of these new structural elements seems crucial for interaction with specific partners, opiate receptors for instance, and may act as a switch that turns on protein activity.
L- to D-amino acid isomerization could be more frequent than initially thought. It cannot be predicted by software tools and is not detectable by any of the standard techniques used in proteomics. It was only discovered when a synthetic peptide with the same sequence of L-amino acids appeared to be biologically inactive. We could be facing a novel strategy of multicellular organisms to circumvent stereochemical limitations imposed by the genetic code in an effort to increase molecular diversity.
Cross-references to ArachnoServer
Cross-references have been added to ArachnoServer, a spider toxin database. ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom.
ArachnoServer is available at http://www.arachnoserver.org/.
The format of the explicit links in the flat file is:
|Resource identifier||ArachnoServer unique identifier.|
|Optional information 1||Toxin name.|
Cross-references to InParanoid
Cross-references have been added to InParanoid, a database of eukaryotic ortholog groups. The InParanoid database is a collection of pairwise comparisons between currently 35 complete proteomes. The InParanoid program uses the pairwise similarity scores, calculated using NCBI-Blast, between two complete proteomes for constructing orthology groups.
InParanoid is available at http://inparanoid.sbc.su.se/.
The format of the explicit links in the flat file is:
|Resource identifier||UniProtKB accession number.|
P10038: DR InParanoid; P10038; -.
Changes concerning keywords
Changes in subcellular location controlled vocabulary
New subcellular location:
- Host multivesicular body
Changes concerning the controlled vocabulary for PTMs
New terms for the feature key 'Cross-link' ('CROSSLNK' in the flat file):
- Glutamyl lysine isopeptide (Gln-Lys) (interchain with K-...)
- Glutamyl lysine isopeptide (Lys-Gln) (interchain with Q-...)
Modified terms for the feature key 'Modified residue' ('MOD_RES' in the flat file):
- Glutamyl 5-glycerylphosphorylethanolamine -> 5-glutamyl glycerylphosphorylethanolamine