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Comparative Study
. 2008 Oct 15:8:286.
doi: 10.1186/1471-2148-8-286.

The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands

Christian Radauer  1 , Peter Lackner, Heimo Breiteneder
Affiliations
Comparative Study

The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands

Christian Radauer et al. BMC Evol Biol. .

Abstract

Background: The major birch pollen allergen, Bet v 1, is a member of the ubiquitous PR-10 family of plant pathogenesis-related proteins. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. In addition, determination of the Bet v 1 structure revealed the existence of a large superfamily of structurally related proteins. In this study, we aimed to identify and classify all Bet v 1-related structures from the Protein Data Bank and all Bet v 1-related sequences from the Uniprot database.

Results: Structural comparisons of representative members of already known protein families structurally related to Bet v 1 with all entries of the Protein Data Bank yielded 47 structures with non-identical sequences. They were classified into eleven families, five of which were newly identified and not included in the Structural Classification of Proteins database release 1.71. The taxonomic distribution of these families extracted from the Pfam protein family database showed that members of the polyketide cyclase family and the activator of Hsp90 ATPase homologue 1 family were distributed among all three superkingdoms, while members of some bacterial families were confined to a small number of species. Comparison of ligand binding activities of Bet v 1-like superfamily members revealed that their functions were related to binding and metabolism of large, hydrophobic compounds such as lipids, hormones, and antibiotics. Phylogenetic relationships within the Bet v 1 family, defined as the group of proteins with significant sequence similarity to Bet v 1, were determined by aligning 264 Bet v 1-related sequences. A distance-based phylogenetic tree yielded a classification into 11 subfamilies, nine exclusively containing plant sequences and two subfamilies of bacterial proteins. Plant sequences included the pathogenesis-related proteins 10, the major latex proteins/ripening-related proteins subfamily, and polyketide cyclase-like sequences.

Conclusion: The ubiquitous distribution of Bet v 1-related proteins among all superkingdoms suggests that a Bet v 1-like protein was already present in the last universal common ancestor. During evolution, this protein diversified into numerous families with low sequence similarity but with a common fold that succeeded as a versatile scaffold for binding of bulky ligands.

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Figures

Figure 1
Figure 1
Structures of representative members of the Bet v 1-like superfamily (A-K) and of oxysterol binding protein (L). A: Birch pollen allergen Bet v 1, Betula verrucosa [PDB:1bv1]; B: STAR-related lipid transport domain of MLN64, Homo sapiens [PDB:1em2]; C: Naphthalene 1,2-dioxygenase, α-chain, C-terminal domain, Pseudomonas putida [PDB:1o7n]; D: Phosphatidylinositol transfer protein alpha, Rattus norvegicus [PDB:1t27]; E: Hypothetical protein NE0264, Nitrosomonas europaea [PDB:1xfs], a member of the AHA1 family; F: Hypothetical protein CC1736, Caulobacter crescentus [PDB:1t17], a member of the polyketide cyclase family; G: Hypothetical protein SMU.440, Streptococcus mutans [PDB:2b79]; H: Hypothetical protein PA1206, Pseudomonas aeruginosa [PDB:2ffs]; I: 2-Oxo-1,2-dihydroquinoline 8-monooxygenase, C-terminal domain, Pseudomonas putida [PDB:1z01], a homotrimeric ring hydroxylase; J: Self-sacrificing resistance protein CalC, Micromonospora echinospora [PDB:1zxf]; K: Hypothetical protein APE2225, Aeropyrum pernix [PDB:2ns9], a member of the CoxG family. L: Oxysterol-binding protein, Saccharomyces cerevisiae [PDB:1zht]. Structures in A-K were coloured according to secondary structure elements homologous to Bet v 1. L was coloured by chain position from blue (N-terminus) to red (C-terminus). Images were generated with UCSF Chimera [61].
Figure 2
Figure 2
Distance-based phylogenetic tree of plant protein sequences related to Bet v 1. The tree was rooted with the only bacterial sequence as outgroup. Uniprot accession numbers of the sequences can be found in Additional file 2.
Figure 3
Figure 3
Distance-based phylogenetic trees of protein sequences from the dicot PR-10 (A) and MLP/RRP (B) subfamilies. Monophyletic groups comprising proteins from single plant families or orders are labelled in A. Uniprot accession numbers of the sequences can be found in Additional file 2.
Figure 4
Figure 4
Distance-based phylogenetic tree of bacterial protein sequences related to Bet v 1. The tree was rooted with homologous plant sequences as outgroup. Bold: DDBDRAFT_0168344 from Dictyostelium discoideum, the only sequence from a species other than plants and bacteria. Uniprot accession numbers of the sequences can be found in Additional file 2.
Figure 5
Figure 5
Secondary structure arrangements of Bet v 1-like superfamily members. Red: β-strands; green: α-helices; filled rectangles: structural elements homologous to corresponding ones in Bet v 1; open rectangles: insertions compared to Bet v 1. Proteins are identified by their PDB accession numbers. Positions of the secondary structure elements are given as provided by the authors in the PDB files.
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