International Immunology, Vol. 15, No. 7, pp. 845-853,
July 2003
© 2003 Japanese Society for Immunology
Bovine IgM antibodies with exceptionally long complementarity-determining region 3 of the heavy chain share unique structural properties conferring restricted VH + V
pairings
1 Departments of Pathobiology and Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada 2 Structural Immunology Laboratory, The Austin Research Institute, Studley Road, Heidelberg, Victoria 3084, Australia
Correspondence to: A. K. Kaushik; E-mail: akaushik{at}uoguelph.ca
Transmitting editor: S. Izui
Naturally occurring antibody repertoires of cattle (Bos taurus) include a group of IgM
antibodies with exceptionally long complementarity-determining region 3 of the heavy chain (CDR3H) segments, containing multiple Cys residues. These massive CDR3H segments will greatly influence the tertiary and quaternary structures of the bovine IgM combining sites. As an antibody’s combining site is formed by both heavy and light chains, we have analyzed the nucleotide sequences and structural properties of the -light chains that pair with µ-heavy chains containing exceptionally long CDR3H. There appears to be an exquisite selective pressure for the use of three V1 genes (V1x and two new V1d and V1e genes) in IgM with unusually long CDR3H. The V1d and V1e genes are similar to each other, but diverge from the other V1 genes into two closely related subfamilies. The available bovine V genes are classified into three V gene families: V1, V2 and V3 based on nucleotide similarity 
80%. Further, analysis of total Ser content and positions of Ser residues in the sequences was found to be sufficient to classify the cattle V1 subfamilies. Patterns of Ser residues differ for V domains from ruminant species (e.g. cattle, sheep and goats) and other mammals (e.g. humans and mice). These ‘Ser signatures’ can be used to track divergent evolution in -light chains. Interestingly, Ser90L in complementarity-determining region 3 of the light chain (CDR3L) occurred in all V domains that pair with VH regions containing exceptionally long CDR3H. A structural role for Ser90L was revealed in homology models of V domains, i.e. to hold the ascending polypeptide of CDR3L in a relatively tight space between the N-terminal segment and residues from CDR1L. The CDR3L of V domains also occupied smaller volumes if paired to VH domains with extremely long CDR3H (48 residues), and were more variable in their conformation and filled larger volumes if CDR3Hs were 
22 residues. Thus, the role of the -light chains in these unusual cattle antibodies is probably to act as a relatively featureless supporting platform for the extremely long CDR3H regions, which undoubtedly are dominantly involved in binding to an antigen.
Keywords: bovine V gene, V1 gene family, VH + V pairing, VDJ rearrangement, VJ rearrangement