Pectate lyases are secreted by pathogens and initiate soft-rot diseases in plants by cleaving polygalacturonate, a major component of the plant cell wall. The three-dimensional structure of pectate lyase C from Erwinia chrysanthemi has been solved and refined to a resolution of 2.2 angstroms. The enzyme folds into a unique motif of parallel beta strands coiled into a large helix. Within the core, the amino acids form linear stacks and include a novel asparagine ladder. The sequence similarities that pectate lyases share with pectin lyases, pollen and style proteins, and tubulins suggest that the parallel beta helix motif may occur in a broad spectrum of proteins.

The structure of EF-Tu-GDP is nearly identical to that of a trypsin-modified form of EF-Tu-GDP, demonstrating conclusively that the protease treatment had not altered any essential structural features. The present structure represents the first view of an ordered Switch I region in EF-Tu-GDP and reveals similarities with two other GTPases complexed with GDP: Ran and ADP-ribosylation factor-1. A comparison of the Switch I regions of the GTP and GDP forms of EF-Tu also reveals that a segment, six amino acids in length, completely converts from an alpha helix in the GTP complex to beta secondary structure in the GDP form. The alpha to beta switch in EF-Tu may represent a prototypical activation mechanism for other protein families.

An analysis of the PelC and PelE structures, belonging to an all parallel beta structural class, reveals novel amino acid side chain interactions, a new type of beta-sandwich and an atypical amino acid composition of parallel beta-sheets. The findings are relevant to three-dimensional structural predictions.

Pels (EC 4.2.2.2) are depolymerizing enzymes that degrade the PGA component of plant cell walls, causing tissue maceration and cell death. The enzymes are normally secreted by phytopathogenic organisms and are the causative agents of virulence in "soft rot" diseases caused by Erwinia sp. (Collmer and Keen, 1986;Kotoujansky, 1987). By sequence analysis, Pels belong to four distinct subfamilies, only two of which appear to be evolutionarily and structurally related. The two related subfamilies, pel-ADE and peZBC, are classified according to various properties, including pI and number of disulfide bonds. Both share three sequence patterns, AxDIKGxxxxVTxS, VxxRxPxxRxGxxHxxxN, and vWiDH (Tamaki et al., 1988;Hinton et al., 1989;Hugouvieux-Cotte-Pattat and Robert-Baudouy, 1992;Barras et al., 1994), which are used to characterize a The authors gratefully acknowledge the support of the U.S. Department of ) and the San Diego Supercomputer Center.

A new type of structural domain, composed of all parallel beta strands, has been observed within the last year. An analysis of the basic types suggests that there are two distinct classes: the parallel beta helices, which belong to a tri beta-strand category, and the beta roll, which belongs to a di beta-strand category. The novel structural features of each class are described and the proteins belonging to each category are summarized. Proteins with the parallel beta helix fold include three pectate lyases and the tailspike protein from P22 phage. Proteins with the beta roll fold include two alkaline proteases. Although the parallel beta composition is emphasized, the same set of proteins share another common structural feature with several other proteins containing alpha helices: the polypeptide backbone is folded into a coiled structure in which each coil has the same 3-dimensional arrangement of a group of secondary structural elements. In addition to parallel beta domains, the other groups include the alpha/beta coiled fold, as represented by ribonuclease inhibitor, and the alpha/alpha coiled fold, as represented by lipovitellin and soluble lytic transglycoslyase. Novel features of the alpha/beta and alpha/alpha coiled folds are summarized.