GE2270A-resistant mutations in elongation factor Tu allow productive aminoacyl-tRNA binding to EF-Tu.GTP.GE2270A complexes.

The antibiotic GE2270A prevents stable complex formation between elongation factor Tu (EF-Tu) and aminoacyl-tRNA (aatRNA). In Escherichia coli we characterized two mutant EF-Tu species with either G257S or G275A that lead to high GE2270A resistance in poly(Phe) synthesis, which at least partially explains the high resistance of EF-Tu1 from GE2270A producer Planobispora rosea to its own antibiotic. Both E. coli mutants were unexpectedly found to bind GE2270A nearly as well as wild-type (wt) EF-Tu in their GTP-bound conformations. Both G257S and G275A are in or near the binding site for the 3' end of aatRNA. The G257S mutation causes a 2.5-fold increase in affinity for aatRNA, whereas G275A causes a 40-fold decrease. In the presence of GE2270A, wt EF-Tu shows a drop in aatRNA affinity of at least four orders of magnitude. EF-Tu[G275S] and EF-Tu[G275A] curtail this drop to about two or one order, respectively. It thus appears that the resistance mutations do not prevent GE2270A from binding to EF-Tu.GTP and that the mutant EF-Tus may accommodate GE2270A and aatRNA simultaneously. Interestingly, in their GDP-bound conformations the mutant EF-Tus have much less affinity for GE2270A than wt EF-Tu. The latter is explained by a recent crystal structure of the EF-Tu.GDP.GE2270A complex, which predicts direct steric problems between GE2270A and the mutated G257S or G275A. These mutations may cause a dislocation of GE2270A in complex with GTP-bound EF-Tu, which then no longer prevents aatRNA binding as in the wt situation. Altogether, the data lead to the following novel resistance scenario. Upon arrival of the mutant EF-Tu.GTP.GE2270.aatRNA complex at the ribosomal A-site, the GTPase centre is triggered. The affinities of aatRNA and GE2270A for the GDP-bound EF-Tu are negligible; the former stays at the A-site for subsequent interaction with the peptidyltransferase centre and the latter two dissociate from the ribosome.

Structure and function of pectic enzymes: virulence factors of plant pathogens.

The structure and function of Erwinia chrysanthemi pectate lysase C, a plant virulence factor, is reviewed to illustrate one mechanism of pathogenesis at the molecular level. Current investigative topics are discussed in this paper.

Structure of an EF-Tu complex with a thiazolyl peptide antibiotic determined at 2.35 A resolution: atomic basis for GE2270A inhibition of EF-Tu.

The structure of a 1:1 molar complex between Escherichia coli elongation factor (EF) Tu-GDP and the cyclic thiazolyl peptide antibiotic, GE2270A, has been determined by X-ray diffraction analysis to a resolution of 2.35 A and refined to a crystallographic refinement factor of 20.6%. The antibiotic binds in the second domain of EF-Tu-GDP, making contact with three segments of amino acids (residues 215-230, 256-264, and 273-277). The majority of the protein-antibiotic contacts are van der Waals interactions. A striking feature of the antibiotic binding site is the presence of a salt bridge, not previously observed in other EF-Tu complexes. The ionic interaction between Arg 223 and Glu 259 forms over the antibiotic and probably accounts for the strong affinity observed between EF-Tu and GE2270A. Arg 223 and Glu 259 are highly conserved, but not invariant throughout the prokaryotic EF-Tu family, suggesting that the antibiotic may bind EF-Tu from some organisms better than others may. Superposition of the antibiotic binding site on the EF-Tu-GTP conformation reveals that one region of the antibiotic would form steric clashes with the guanine nucleotide-binding domain in the GTP, but not the GDP, conformation. Another region of the antibiotic binds to the same site as the aminoacyl group of tRNA. Together with prior biochemical studies, the structural findings confirm that GE2270A inhibits protein synthesis by blocking the GDP to GTP conformational change and by directly competing with aminoacyl-tRNA for the same binding site on EF-Tu. In each of the bacterial strains that are resistant to GE2270A, the effect of a site-specific mutation in EF-Tu could explain resistance. Comparison of the GE2270A site in EF-Tu with sequence homologues, EF-G and EF-1alpha, suggests steric clashes that would prevent the antibiotic from binding to translocation factors or to the eukaryotic equivalent of EF-Tu. Although GE2270A is a potent antibiotic, its clinical efficacy is limited by its low aqueous solubility. The results presented here provide the details necessary to enhance the solubility of GE2270A without disrupting its inhibitory properties.

Structure of a plant cell wall fragment complexed to pectate lyase C.

The three-dimensional structure of a complex between the pectate lyase C (PelC) R218K mutant and a plant cell wall fragment has been determined by x-ray diffraction techniques to a resolution of 2.2 A and refined to a crystallographic R factor of 18.6%. The oligosaccharide substrate, alpha-D-GalpA-([1-->4]-alpha-D-GalpA)3-(1-->4)-D-GalpA , is composed of five galacturonopyranose units (D-GalpA) linked by alpha-(1-->4) glycosidic bonds. PelC is secreted by the plant pathogen Erwinia chrysanthemi and degrades the pectate component of plant cell walls in soft rot diseases. The substrate has been trapped in crystals by using the inactive R218K mutant. Four of the five saccharide units of the substrate are well ordered and represent an atomic view of the pectate component in plant cell walls. The conformation of the pectate fragment is a mix of 21 and 31 right-handed helices. The substrate binds in a cleft, interacting primarily with positively charged groups: either lysine or arginine amino acids on PelC or the four Ca2+ ions found in the complex. The observed protein-oligosaccharide interactions provide a functional explanation for many of the invariant and conserved amino acids in the pectate lyase family of proteins. Because the R218K PelC-galacturonopentaose complex represents an intermediate in the reaction pathway, the structure also reveals important details regarding the enzymatic mechanism. Notably, the results suggest that an arginine, which is invariant in the pectate lyase superfamily, is the amino acid that initiates proton abstraction during the beta elimination cleavage of polygalacturonic acid.

Sequence profile of the parallel beta helix in the pectate lyase superfamily.

The parallel beta helix structure found in the pectate lyase superfamily has been analyzed in detail. A comparative analysis of known structures has revealed a unique sequence profile, with a strong positional preference for specific amino acids oriented toward the interior of the parallel beta helix. Using the unique sequence profile, search patterns have been constructed and applied to the sequence databases to identify a subset of proteins that are likely to fold into the parallel beta helix. Of the 19 families identified, 39% are known to be carbohydrate-binding proteins, and 50% belong to a broad category of proteins with sequences containing leucine-rich repeats (LRRs). The most striking result is the sequence match between the search pattern and four contiguous segments of internalin A, a surface protein from the bacterial pathogen Listeria monocytogenes. A plausible model of the repetitive LRR sequences of internalin A has been constructed and favorable 3D-1D profile scores have been calculated. Moreover, spectroscopic features characteristic of the parallel beta helix topology in the pectate lyases are present in the circular dichroic spectrum of internalin A. Altogether, the data support the hypothesis that sequence search patterns can be used to identify proteins, including a subset of LRR proteins, that are likely to fold into the parallel beta helix.

The tree-dimensional structure of aspergillus niger pectin lyase B at 1.7-A resolution.

The three-dimensional structure of Aspergillus niger pectin lyase B (PLB) has been determined by crystallographic techniques at a resolution of 1.7 A. The model, with all 359 amino acids and 339 water molecules, refines to a final crystallographic R factor of 16.5%. The polypeptide backbone folds into a large right-handed cylinder, termed a parallel beta helix. Loops of various sizes and conformations protrude from the central helix and probably confer function. The largest loop of 53 residues folds into a small domain consisting of three antiparallel beta strands, one turn of an alpha helix, and one turn of a 3(10) helix. By comparison with the structure of Erwinia chrysanthemi pectate lyase C (PelC), the primary sequence alignment between the pectate and pectin lyase subfamilies has been corrected and the active site region for the pectin lyases deduced. The substrate-binding site in PLB is considerably less hydrophilic than the comparable PelC region and consists of an extensive network of highly conserved Trp and His residues. The PLB structure provides an atomic explanation for the lack of a catalytic requirement for Ca2+ in the pectin lyase family, in contrast to that found in the pectate lyase enzymes. Surprisingly, however, the PLB site analogous to the Ca2+ site in PelC is filled with a positive charge provided by a conserved Arg in the pectin lyases. The significance of the finding with regard to the enzymatic mechanism is discussed.

An alpha to beta conformational switch in EF-Tu.

BACKGROUND: The bacterial elongation factor EF-Tu recognizes and transports aminoacyl-tRNAs to mRNA-programmed ribosomes. EF-Tu shares many structural and functional properties with other GTPases whose conformations are regulated by guanine nucleotides. RESULTS: An intact form of Escherichia coli EF-Tu complexed with GDP has been crystallized in the presence of the EF-Tu-specific antibiotic GE2270 A. The three-dimensional structure has been solved by X-ray diffraction analysis and refined to a final crystallographic R factor of 17.2% at a resolution of 2.5 A. The location of the GE2270 A antibiotic-binding site could not be identified. CONCLUSIONS: 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.

Differential effect of site-directed mutations in pelC on pectate lyase activity, plant tissue maceration, and elicitor activity.

Oligonucleotide site-directed mutations were introduced into the pelC gene of Erwinia chrysanthemi EC16 that directed single or double amino acid changes affecting disulfide linkages, calcium binding, catalysis, and protein folding. Subsequent characterization of the purified PelC mutant proteins demonstrated that pectinolytic function involves amino acids located near the calcium binding site rather than those surrounding an invariant vWiDH sequence. Wild-type PelC and the tested mutant proteins generally macerated plant tissue in proportion to their specific pectinolytic activity in vitro. However, some mutants gave higher maceration activity in plant tissue and elicited greater production of the phytoalexin, glyceollin, in soybean cotyledons than predicted by their in vitro pectinolytic activity. Most notable in this regard were three different mutations at lysine 172 with greatly reduced pectinolytic activity but as much elicitor activity as the wild-type protein. PelE macerated plant tissue 10 times more efficiently than PelC, as observed previously, but surprisingly showed equal activity in the elicitor assay. The results indicate that factors other than pectinolytic activity per se are involved in plant tissue maceration and elicitor activity.

The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.

The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics techniques to a resolution of 2.2 A and an R factor (an agreement factor between observed structure factor amplitudes) of 16.1%. The final model consists of all 355 amino acids and 157 water molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.721[deg] for bond angles. The structure of PelE bound to a lanthanum ion, which inhibits the enzymatic activity, has also been refined and compared to the metal-free protein. In addition, the structures of pectate lyase C (PelC) in the presence and absence of a lutetium ion have been refined further using an improved algorithm for identifying waters and other solvent molecules. The two putative active site regions of PelE have been compared to those in the refined structure of PelC. The analysis of the atomic details of PelE and PelC in the presence and absence of lanthanide ions provides insight into the enzymatic mechanism of pectate lyases.

A complex profile of protein elongation: translating chemical energy into molecular movement.

The recently solved structures of the protein elongation factor complexes, EF-Tu-GDPNP-phenylalanyl-tRNA and EF-T-Ts, complete the atomic profile of four EF-Tu conformational states. As a set, the three-dimensional structures suggest an atomic model for movement during protein elongation and, by molecular mimicry with EF-G, translocation as well.

Circular dichroism of the parallel beta helical proteins pectate lyase C and E.

The pectate lyases, PelC and PelE, have an unusual folding motif, known as a parallel beta-helix, in which the polypeptide chain is coiled into a larger helix composed of three parallel beta-sheets connected by loops having variable lengths and conformations. Since the regular secondary structure consists almost entirely of parallel beta-sheets these proteins provide a unique opportunity to study the effect of parallel beta-helical structure on circular dichroism (CD). We report here the CD spectra of PelC and PelE in the presence and absence of Ca2+, derive the parallel beta-helical components of the spectra, and compare these results with previous CD studies of parallel beta-sheet structure. The shape and intensity of the parallel beta-sheet spectrum is distinctive and may be useful in identifying other proteins that contain the parallel beta-helical folding motif.

Functional implications of structure-based sequence alignment of proteins in the extracellular pectate lyase superfamily.

Pectate lyases are plant virulence factors that degrade the pectate component of the plant cell wall. The enzymes share considerable sequence homology with plant pollen and style proteins, suggesting a shared structural topology and possibly functional relationships as well. The three-dimensional structures of two Erwinia chrysanthemi pectate lyases, C and E, have been superimposed and the structurally conserved amino acids have been identified. There are 232 amino acids that superimpose with a root-mean-square deviation of 3 A or less. These amino acids have been used to correct the primary sequence alignment derived from evolution-based techniques. Subsequently, multiple alignment techniques have allowed the realignment of other extracellular pectate lyases as well as all sequence homologs, including pectin lyases and the plant pollen and style proteins. The new multiple sequence alignment reveals amino acids likely to participate in the parallel beta helix motif, those involved in binding Ca2+, and those invariant amino acids with potential catalytic properties. The latter amino acids cluster in two well-separated regions on the pectate lyase structures, suggesting two distinct enzymatic functions for extracellular pectate lyases and their sequence homologs.

Protein motifs. 3. The parallel beta helix and other coiled folds.

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.

Structure-based multiple alignment of extracellular pectate lyase sequences.

Pectate lyases are secreted virulence factors which degrade the pectate component of plant cell walls. The evolutionary-based multiple alignment of extracellular pectate lyases has been corrected using three-dimensional structural information derived from Erwinia chyrsanthemi pectate lyases C and E. The new multiple alignment reveals invariant amino acids likely to be involved in two different enzymatic functions.

The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).

The crystal structure of pectate lyase C (EC 4.2.2.2) from the enterobacterium Erwinia chrysanthemi (PelC) has been refined by molecular dynamics techniques to a resolution of 2.2 A to an R factor of 17.97%. The final model consists of 352 of the total 353 amino acids and 114 solvent molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.768[deg] for bond angles. The structure of PelC bound to the lanthanide ion lutetium, used as a calcium analog, has also been refined. Lutetium inhibits the enzymatic activity of the protein, and in the PelC-lutetium structure, the ion binds in the putative calcium-binding site. Five side-chain atoms form ligands to the lutetium ion. An analysis of the atomic-level model of the two protein structures reveals possible implications for the enzymatic mechanism of the enzyme.

Parallel beta-domains: a new fold in protein structures.

A new type of structural domain, composed of parallel beta-strands folded into a coiled structure, has been observed in several protein structures within the past year. An analysis of the basic motif indicates that there are two distinct types, with variations likely to be discovered in the future.

The Three-Dimensional Structure of Pectate Lyase E, a Plant Virulence Factor from Erwinia chrysanthemi.

The three-dimensional structure of pectate lyase E (PelE) has been determined by crystallographic techniques at a resolution of 2.2 A. The model includes all 355 amino acids but no solvent, and refines to a crystallographic refinement factor of 20.6%. The polypeptide backbone folds into a large right-handed cylinder, termed a parallel [beta] helix. Loops of various sizes and conformations protrude from the central helix and probably confer function. A putative Ca2+-binding site as well as two cationic sites have been deduced from the location of heavy atom derivatives. Comparison of the PelE and recently determined pectate lyase C (PelC) structures has led to identification of a putative polygalacturonate-binding region in PelE. Structural differences relevant to differences in the enzymatic mechanism and maceration properties of PelE and PelC have been identified. The comparative analysis also reveals a large degree of structural conservation of surface loops in one region as well as an apparent aromatic specificity pocket in the amino-terminal branch. Also discussed is the sequence and possible functional relationship of the pectate lyases with pollen and style plant proteins.

The ABC of EF-G.

The recently solved crystal structures of Thermus thermophilus elongation factor G, with and without GDP, reveal a protein of five domains with surprising features which can be correlated with biochemical data to suggest probable functional roles.

Extension of the diffraction resolution of crystals.

The diffraction resolution of crystals of the guanine nucleotide-exchange factor complex, EF-Tu-Ts, has been extended from 5.0 to 2.5 A by lowering the solvent content in the crystals as well as the temperature of data collection. The common form of EF-Tu-Ts crystal belongs to space group P2(1)2(1)2(1) with a = 81.1, b = 109.9, c = 207.5 A and has a solvent content of 61%. The crystals diffract to a resolution of 5.0 A at 293 K and 4.0 A at 273 K. When cryoprotective agents are slowly diffused into the crystals, the cell constants shrink to a = 74.4, b = 109.9, c = 198.7 A and the solvent content falls to 55%. After the cryoprotective agent has been added, the crystals diffract to 2.7 A resolution at 293 or 273 K and 2.5 A at 250 K. X-ray diffraction data, collected before and after the transformation of individual EF-Tu-Ts crystals, demonstrate that a large percentage of the improvement in diffraction resolution is due solely to the addition of cryoprotective agents. The transfer procedures for the successful introduction of cryoprotective agents into EF-Tu-Ts crystals as well as the general applicability to other crystal systems will be discussed.