A nomenclature is described for restriction endonucleases, DNA methyltransferases, homing endonucleases and related genes and gene products. It provides explicit categories for the many different Type II enzymes now identi®ed and provides a system for naming the putative genes found by sequence analysis of microbial genomes.

The crystal structure of the Fab of the galactan-binding immunoglobulin J539 (a mouse IgA,kappa) has been determined at a resolution of approximately 2.6 A by X-ray diffraction. The starting model was that obtained from the real space search described previously (Navia, M.A., Segal, D.M., Padlan, E.A., Davies, D.R., Rao, D.N., Rudikoff, S. and Potter, M. "Crystal structure of galactan-binding mouse immunoglobulin J539 Fab at 4.5 A resolution." Proc. Nat. Acad. Sci. USA, 76:4071-4074, 1979). This Fab structure has now been refined by restrained least-squares procedures to an R-value of 19% for the 11,690 unique reflections between 8.0 A and 2.6 A. The rms deviation from ideal bond lengths is 0.025 A. The overall structure differs from McPC603 Fab, another mouse IgA,kappa antibody, in that the elbow bend, relating the variable and constant parts of the molecule, is 145 degrees vs. 133 degrees for McPC603. The region of the molecule expected to be the antigen binding site contains a large cavity with two clefts leading away from it. This has been fitted with a model of an oligo-galactan.

We have determined the variable region sequences of four heavy chains from #(1-6)D-galactan-binding myeloma proteins. Two of these proteins are identical to position 100 which is located in the third complementarity-determining region (CDR-3). The remaining two differ at a total of 8 positions over the first 100 amino acids, and all of the differences can be explained by single-base mutations at the DNA level. When an assessment is made of the protein segment following CDR-3, which has been termed "J segment" or "FR4," a completely different pattern of variation is observed. The J segments from the four proteins can be divided into two sets. Members of each set share a series of linked amino acids not found in members of the alternative set. The two proteins identical to position 100 have J segments from the two different sets, suggesting that recombination has occurred between V and J genes. 2, 3). The sequence variations in CDR provide the molecular basis for generating a large number of antibody-combining sites. The remainder of the V region, the framework portion, serves to bring the CDR into three-dimensional proximity to form the antigen-binding surface. Following the elucidation of immunoglobulin structure, interest has now been turned to the intriguing problem of the organization and expression of the genes coding for this unique set of molecules. From sequencing studies of myeloma proteins from the BALB/c mouse it is clear that an increasingly large number of subgroups or isotypes for both K (4, 5) and heavy (6) chains can be identified based on a number of amino acid differences in the NH2-terminal portion of these chains. Each of these subgroups or isotypes presumably would require at least one germ-line gene to code for the members of a given isotype. McKean et al. (7), in a detailed analysis of eight members of a single isotype, have presented data indicating the existence of multiple closely related germ-line genes coding for these proteins. Similar results have been found with the same isotype group in NZB mice (8). Studies at the DNA level by Seidman et al. (9), using probes to two K chain V regions, have identified at least six to nine genes that can be isolated by using either probe. The set defined by the first probe is completely distinct from that reactive with the second probe. The results of these two types of experiments strongly suggest the existence of a large number of germ-line genes. For example, if there were 100 isotypes for K chains and each isotype reflected 10 genes, then 103 germ-line genes would be required to code for these structures.With the existence of an apparently large number of germline genes, the questions of their organization and expression remain to be explored. In contrast to the large number of germ-line V region genes, it is generally agreed that very few copies exist of each of the C region genes. Therefore, we need to understand not only the organization and expression of V region genes but also the mechanism by which a single C region apparently can...

Immunoglobulin K light chains are coded for by at least three distinct gene segments designated variable, joining, and constant. The joining gene codes for the 13 amino acid segment linking the variable and constant regions. This peptide includes the last amino acid (96) in the third complementarity-determining region and thus could introduce structural diversity. We have determined the light chain variable region sequences from three myeloma proteins with P(1,6)galactan-binding specificity, bringing to six the number of light chains sequenced from proteins demonstrating this specificity. Five of these have isoleucine at position 96 and the sixth tryptophan. This substitution appears to be accommodated with no significant change in association constant for a 19(1,6)galactan hapten. Additionally, as many as nine substitutions are found in both light and heavy chain complementarity-determining regions between members of this group-although only minimal variations in hapten binding affinity are observed. The isoleucine found at position 96 in five of the X chains could not be coded for by any of the joining gene nucleotide. sequences previously observed and would require a novel nucleotide sequence at the recombination site between variable and joining genes to produce the observed protein structure. Alternatively, there may exist joining gene segments not yet detected. The study of antibody structure and diversity has long been of great interest in the field of immunology. The immunoglobulin molecule is composed of two polypeptide chains designated light (L) and heavy (H), each of which is encoded on a separate chromosome (1). Each of these two chains in turn is coded for by at least three distinct genetic regions termed variable (V), constant (C), and joining (J). The V regions of both H and L chains exhibit primary amino acid sequence differences that are responsible for the great variety of antigen binding specificities exhibited by vertebrate organisms. All L chain C regions may be divided into two classes, K and X; the corresponding region in heavy chains may represent several classes-i.e., jA y, a, 6, and e.Recent studies at both the protein (2-4) and nucleic acid levels (5, 6) have identified a third segment of the immunoglobulin chain, the J segment which bridges the V and C regions. The size and boundaries of this segment have been defined for mouse K chains and include the last residue in the third complementarity-determining region. A corresponding J segment has been identified in H chains by protein sequence determination (4, 7) and by nucleic acid analysis (8).For a number of years this laboratory has attempted to explore various aspects of antibody structure and diversity by analyzing groups of antigen-binding myeloma proteins. One such group is composed of proteins with binding specificity for 3(1,6)-linked galactan moieties. Six of these proteins have been studied in terms of specificity (9, 10), structure (3, 4, 11), and idiotypy (12). We have reported the L chain V region sequences from ...

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