Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor.

BACKGROUND: Hevamine is a member of one of several families of plant chitinases and lysozymes that are important for plant defence against pathogenic bacteria and fungi. The enzyme can hydrolyze the linear polysaccharide chains of chitin and peptidoglycan. A full understanding of the structure/function relationships of chitinases might facilitate the production of transgenic plants with increased resistance towards a wide range of pathogens. RESULTS: The crystal structure of hevamine has been determined to a resolution of 2.2 A, and refined to an R-factor of 0.169. The enzyme possesses a (beta alpha)8-barrel fold. An inhibitor binding study shows that the substrate-binding cleft is located at the carboxy-terminal end of the beta-barrel, near the conserved Glu127. Glu127 is in a position to act as the catalytic proton donor, but no residue that might stabilize a positively charged oxocarbonium ion intermediate was found. A likely mechanism of substrate hydrolysis is by direct attack of a water molecule on the C1 atom of the scissile bond, resulting in inversion of the configuration at C1. CONCLUSIONS: The structure of hevamine shows a completely new lysozyme/chitinase fold and represents a new class of polysaccharide-hydrolyzing (beta alpha)8-barrel enzymes. Because the residues conserved in the family to which hevamine belongs are important for maintaining the structure of the (beta alpha)8-barrel, all members of the family, including fungal, bacterial and insect chitinases, are likely to share this architecture. The crystal structure obtained provides a basis for protein engineering studies in this family of chitinases.

Primary structures of pancreatic ribonucleases from Bovidae. Impala, Thomson's gazelle, nilgai and water buffalo.

The amino acid sequences of the pancreatic ribonucleases from impala Thomson's gazelle, nilgai and two types of water buffalo were studied from several enzymic digests. Peptides were positioned by homology with other ribonucleases of known sequence. Only peptides that differ in amino acid composition from the corresponding peptides of ox and goat ribonuclease were sequenced. The primary structures of pancreatic ribonucleases from 11 species of the Bovidae family are known to date. The evolutionary rate of bovid ribonucleases is 2--3 times lower than the average rate observed in all mammals. A possible explanation is that the presence of a stable symbiotic system in the rumen of grass-eating ruminants has caused a slowing down of the evolutionary rate of pancreatic ribonuclease in this taxon. The subfamily of the Bovinae (five species) exhibits a slightly higher evolutionary rate; most replacements in the Bovinae occur near residues 34--36, the most commonly observed carbohydrate attachment site in ribonucleases.

The amino acid sequence of topi pancreatic ribonuclease.

Pancreatic tissue from topi (Damaliscus korrigum) contains three ribonuclease components in a ratio of 8:22:70. Two components are glycosidated, whereas the third one does not contain carbohydrate. The amino acid sequence of topi ribonuclease A was deduced from a tryptic digest of the performic acid-oxidized protein. Peptides were positioned by homology with other bovid ribonucleases. Only peptides that differed in amino acid composition from the corresponding peptides of bovine ribonuclease were sequenced. The evidence obtained for the sequence of residues 67-73 is incomplete. Among the bovid ribonucleases (cow, bison, eland, sheep, goat and gnu), topi ribonuclease shows the closest resemblance with sheep and goat ribonucleases; except that the glutamic acid residue at position 103 in the ribonucleases from sheep and goat is substituted by a lysine residue in topi. Topi ribonucleases A and B differ only in the presence of carbohydrate attached to asparagine 34.

Steady-state enzyme kinetics of the pancreatic ribonucleases from five mannalian species.

The kinetic parameters Km, k+2 and k+2/Km of the pancreatic ribonucleases (EC 3.1.4.22) from cow, giraffe, horse, rat and lesser rorqual have been determined, using 2',3'-cyclic cytidine monophosphate and 2',3'-cuclic uridine monophosphate as substrates. No large differences were found between the activities of the five enzymes. The relative differences between the activities of the five enzymes are mainly due to differences in the rates of hydrolysis and not to differences in the affinities for the substrates.

The primary structures of pancreatic ribonucleases from African porcupine and casiragua, two hystricomorph rodent species.

The amino acid sequences of the pancreatic ribonucleases from African porcupine (Hystrix cristata) and casiragua (Proechimys guairae, a caviomorph rodent species related to the coypu) were determined. The ribonucleases were isolated form minces of pancreatic tissue which had been used for the extraction of the insulins. The results of the sequence determinations of residues 67-78 in both enzymes were ambiguous. Therefore, homology with other ribonucleases has been used in deriving these sequences. At position 94 aspartic acid was found, while all other ribonuclease sequenced to date have asparagine at this position. This may indicate a specific deamidation as a result of the acidic conditions during the extraction of insulin. The amino acid sequence of African porcupine ribonuclease shows a close relationship with those of the South-American caviomorph rodents, which implies that the hystricomorph suborder of the rodents, to which both the African porcupine and the caviomorphs belong, is a natural (evolutionary) taxon. Both porcupine and casiragua ribonuclease are glycoproteins with complex-type carbohydrate chains attached to asparagine-34.

Studies on the covalent structure of eland pancreatic ribonuclease.

Studies on the covalent structure of eland (Taurotragus oryx) pancreatic ribonuclease have been performed on tryptic and thermolysin digests. The first 45 residues have been determined with a Beckman sequencer. From the remaining part of the sequence only those peptides were sequenced that differed in amino acid composition with the corresponding peptide of bovine ribonuclease. Eland pancreatic ribonuclease differs in four positions from bovine pancreatic ribonuclease A, but more differences due to a different state of amidation may be present. The absence of an Asn-X-Thr/Ser sequence in the covalent structure of eland ribonuclease (asparagine 34 has been substituted by aspartic acid) explains the absence of a glycosidated component in eland ribonuclease.

Reinvestigation of the primary structures of red deer and roe deer pancreatic ribonuclease and proline sites in mammalian ribonucleases.

The sequences of amino acid residues 15-23 of red deer (Cervus elaphus) and roe deer (Capreolus capreolus) pancreatic ribonuclease and the identity of residue 99 in roe deer ribonuclease are corrected. Earlier results are explained by the cleavage of an Asp-Pro bond in both enzymes during the treatment with CNBr in 70% formic acid and by wrong interpretations of amino acid analyses. Proline residues, which occur at a number of positions in several mammalian ribonucleases, can be accommodated in a model of bovine ribonuclease S without disrupting the conformation of the main chain.

Isolation, properties and primary structure of coypu and chinchilla pancreatic ribonuclease.

Pancreatic ribonucleases from the hystricomorph rodent species: coypu and chinchilla were isolated using chromatography on carboxymethyl-cellulose. The amino acid sequences were determined from tryptic digests of the aminoethylated proteins. The tryptic peptides were positioned in the sequence by homology with other pancreatic ribonucleases. Coypu pancreas contains one carbohydrate-containing ribonuclease component. From chinchilla pancreas two carbohydrate-containing ribonuclease components were obtained; one homogeneous and the other heterogeneous. The latter differs from the first in being more acidic; it exhibits heterogeneity both in its carbohydrate moiety (glycopeptides both with and without sialic acid were isolated) and in amino acid sequence (probably glycine at position 32 has been partially substituted by aspartic acid). In both ribonucleases the carbohydrate is attached to asparagine 34. Earlier results on the titration behaviour of histidine residues in both proteins obtained by nuclear magnetic resonance spectroscopy are discussed. An ion bridge between the invariant glutamic acid 49 and histidine 80 may explain the high pK value of the latter.

Dimerization of an antigenic peptide leads to strong interaction with its antibody.

A sequential epitope reacting with a monoclonal antibody against Panulirus interruptus hemocyanin was localized in the C-terminal CNBr peptide. As the antibody reacted with about equal affinity with different subunits of this and with hemocyanin from another spiny lobster, Palinurus vulgaris, the epitope was assigned to a conserved sequence region. The CNBr peptide, which was linked to another peptide via a disulfide bridge, was reduced and reoxidized. As a result, not the heterodimer but only the two disulfide-linked homodimers were formed. The dimeric C-terminal peptide had a much higher affinity for the monoclonal antibody than the monomeric peptide. This may be explained by the presence of two independent mobile interaction sites in each of the two reacting molecules.

Nucleic acid-protein interactions. Degradation of double-stranded RNA by glycosylated ribonucleases.

1. Extensively glycosylated ribonucleases, like the enzymes from pig and horse pancreas, show a much higher activity on double-stranded RNAs than similarly charged, carbohydrate-free RNAases under stranded assay conditions (relatively high salt concentrations). Glycosylated pig and horse pancreas RNAases also show a larger destabilizing effect on double-stranded poly[d(A-T)] X poly[d(A-T)], than that displayed by bovine RNAase A under these conditions. Both activities show a similar dependence on the ionic strength of the medium. 2. A partial enzymic removal of the heterosaccharide side chains from pig and horse RNAases reduces but their degradative activity on double-stranded RNA and their destabilizing action on poly[d(A-T)] X poly[d(A-T)]. 3. These results are tentatively correlated with a modification of the microenvironment of the enzyme protein caused by its extensive glycosylation.

Demonstration by mass spectrometry that pseudo-hevein and hevein have ragged C-terminal sequences.

The primary structure of pseudo-hevein, a minor hevein component from the latex of the rubber tree, Hevea brasiliensis, was determined. Six differences with the sequence of the major hevein component were found, one of which is a replacement of tryptophan by tyrosine in the carbohydrate binding region of the molecule. Analysis by ion-spray mass spectrometry showed that pseudo-hevein has a heterogeneous C-terminal extension of several glycine residues and that hevein itself also contains minor components with additional C-terminal amino-acid residues. A seventh difference between the two sequences occurs in these extensions.

Kinetic studies on turtle pancreatic ribonuclease: a comparative study of the base specificities of the B2 and P0 sites of bovine pancreatic ribonuclease A and turtle pancreatic ribonuclease.

Kinetic constants for the transesterification of eight dinucleoside phosphates CpX and UpX by bovine and turtle pancreatic ribonuclease were determined. Both ribonucleases have a preference for purine nucleotides at the position X. However, bovine ribonuclease, like other mammalian ribonucleases, prefers 6-amino bases at this site, while turtle ribonuclease prefers 6-keto bases. This difference in specificity at the B2 site may be explained by the substitution of glutamic acid at position 111 by valine in turtle ribonuclease. These results have been confirmed by inhibition studies with the four nucleoside triphosphates. Inhibition studies with pT and pTp showed that a cationic binding group (P0) for the 5'-phosphate of the pyrimidine nucleotides bound at the primary B1 site is present in turtle ribonuclease, although lysine at position 66 in bovine ribonuclease is absent in turtle ribonuclease. However, the side chain of lysine 122 in turtle ribonuclease is probably located in the correct position to take over the role as cationic P0 site.

Primary structure of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens.

The amino acid sequence of the p-hydroxybenzoate hydroxylase (4-hydroxybenzoate,NADPH:oxygen oxidoreductase (3-hydroxylating), EC 1.14.13.2) monomer from Pseudomonas fluorescens has been determined. The sequence was elucidated by a combination of the results from an X-ray crystallographic study at 0.25 nm resolution (Wierenga, R.K., de Jong, R.J., Kalk, K.H., Hol, W.G.J. and Drenth, J. (1979) J. Mol. Biol. 131, 55-73) and from protein sequence analysis. The polypeptide chain of the monomer contains 394 amino acids and has a molecular weight of 44 299.

Ribonucleases from rat and bovine liver: purification, specificity and structural characterization.

The presence of four members of the pyrimidine-specific ribonuclease superfamily was demonstrated in rat liver. Three of them (RL1, RL2 and RL3) were purified and showed ribonuclease activity at pH 7.5 with yeast RNA as substrate. RL1 is identical to rat pancreatic ribonuclease (ribonuclease 1). N-terminal sequence analysis showed the presence of the native protein and several N-terminally degraded components. RL2 and RL3 were N-terminally blocked proteins. After acidic cleavage or CNBr digestion, several parts of their sequences were determined. RL2 has high sequence similarity with neurotoxin-type ribonucleases (ribonucleases 2, 3 and 6). The amino acid sequence of rat liver-type ribonuclease (ribonuclease 4) was determined from a liver cDNA library. It differs at about 20% of the amino acid positions from other mammalian liver-type ribonucleases. The sequence of a peptide of RL3 was identical to that derived from the cDNA sequence of the liver-type ribonuclease. A contaminant of the RL3 fraction had a high sequence similarity with mouse and other mammalian angiogenins. Bovine, porcine and rat liver-type ribonucleases showed a strong preference for poly(U) over poly(C). This preference is a unique property of the liver-type enzymes of the ribonuclease superfamily.

Ruminant brain ribonucleases: expression and evolution.

Molecular evolutionary analyses of mammalian ribonucleases have shown that gene duplication events giving rise to three paralogous genes occurred in ruminant ancestors. One of these genes encodes a ribonuclease identified in bovine brain. A peculiar feature of this enzyme and orthologous sequences in other ruminants are C-terminal extensions consisting of 17-27 amino acid residues. Evidence was obtained by Western blot analysis for the presence of brain-type ribonucleases in brain tissue not only of ox, but also of sheep, roe deer and chevrotain (Tragulus javanicus), a member of the earliest diverged taxon of the ruminants. The C-terminal extension of brain-type ribonuclease from giraffe deviates much in sequence from orthologues in other ruminants, due to a change of reading frame. However, the gene encodes a functional enzyme, which could be expressed in heterologous systems. The messenger RNA of bovine brain ribonuclease is not only expressed at a high level in brain tissue but also in lactating mammary gland. The enzyme was isolated and identified from this latter tissue, but was not present in bovine milk, although pancreatic ribonucleases A and B could be isolated from both sources. This suggests different ways of secretion of the two enzyme types, possibly related to structural differences. The sequence of the brain-type RNase from chevrotain suggests that the C-terminal extensions of ruminant brain-type ribonucleases originate from deletions in the ancestral DNA (including a region with stop codons), followed by insertion of a 5-8-fold repeated hexanucleotide sequence, coding for a proline-rich polypeptide.

Crystallization of hevamine, an enzyme with lysozyme/chitinase activity from Hevea brasiliensis latex.

Hevamine, an enzyme with both lysozyme and chitinase activity, was isolated and purified from Hevea brasiliensis (rubber tree) latex. The enzyme (molecular weight 29,000) is homologous to certain "pathogenesis-related" proteins from plants, but not to hen egg-white or phage T4 lysozyme. To investigate the atomic details of the substrate specificity and the cause for hevamine's low pH optimum (pH 4.0), we have crystallized two hevamine isozymes as a first step towards a high-resolution X-ray structure determination. Suitable crystals were obtained at room temperature from hanging drop experiments by vapor diffusion against 1.7 M to 3.4 M-NaCl (pH 5.0 to 9.0) for the major isozyme, and by vapor diffusion against 2.5 M to 4.3 M-NaCl (pH 5.0 to 8.0) for the minor one. Both isozymes give the same crystal morphology and space group. Their space group is P2(1)2(1)2(1) with cell dimensions a = 82.3 A, b = 58.1 A and c = 52.5 A (1 A = 0.1 nm). The crystals diffract to at least 2.0 A resolution.

Seminal-type ribonuclease genes in ruminants, sequence conservation without protein expression?

Bovine seminal ribonuclease (BS-RNase) is an interesting enzyme both for functional and structural reasons. The enzyme is the product of a gene duplication that occurred in an ancestral ruminant. It is possible to demonstrate the presence of seminal-type genes in all other investigated ruminant species, but they are not expressed and show features of pseudogenes. In this paper we report the determination of two pancreatic and one seminal-type ribonuclease gene sequences of swamp-type water buffalo (Bubalus bubalis). The two pancreatic sequences encode proteins with identical amino acid sequences as previously determined for the enzymes isolated from swamp-type and river-type water buffalo, respectively. The seminal-type sequence has no pseudogene features and codes for an enzyme with no unusual features compared with the active bovine enzyme, except for the replacement of one of the cysteines which takes part in the two intersubunit disulfide bridges. However, Western blotting demonstrates the presence of only small amounts of the pancreatic enzymes in water buffalo semen, suggesting that also in this species the seminal-type sequence is not expressed. But it is still possible that the gene is expressed somewhere else in the body or during development. Reconstruction of seminal-type ribonuclease sequences in ancestors of Bovinae and Bovidae indicates no serious abnormalities in the encoded proteins and leads us to the hypothesis that the ruminant seminal-type ribonuclease gene has not come to expression during most of its evolutionary history, but did not exhibit a high evolutionary rate that is generally observed in pseudogenes.

Secretory ribonuclease genes and pseudogenes in true ruminants.

Mammalian pancreatic ribonucleases (RNase) form a family of extensively studied homologous proteins. Phylogenetic analyses, based on the primary structures of these enzymes, indicated that the presence of three homologous enzymes (pancreatic, seminal and brain ribonucleases) in the bovine species is due to gene duplication events, which occurred during the evolution of ancestral ruminants. In this paper the sequences are reported of the coding regions of the orthologues of the three bovine secretory ribonucleases in hog deer and roe deer, two deer species belonging to two different subfamilies of the family Cervidae. The sequences of the 3' untranslated regions of the three different secretory RNase genes of these two deer species and giraffe are also presented. Comparison of these and previously determined sequences of ruminant ribonucleases showed that the brain-type enzymes of giraffe and these deer species exhibit variations in their C-terminal extensions. The seminal-type genes of giraffe, hog deer and roe deer show all the features of pseudogenes. Phylogenetic analyses, based on the complete coding regions and parts of the 3' untranslated regions of the three different secretory ribonuclease genes of ox, sheep, giraffe and the two deer species, show that pancreatic, seminal- and brain-type RNases form three separate groups.

Presence of a basic amino acid residue at either position 66 or 122 is a condition for enzymic activity in the ribonuclease superfamily.

Some members of the ribonuclease superfamily differ at more than 50% of the amino acid positions. Although the three-dimensional structures probably are very similar and the active-site residues have been conserved, other substrate-binding regions have changed considerably. Several proteins in the superfamily are active ribonucleases while other exhibit practically no enzymic activity. The presence of a basic residue at either position 66 or 122 appears to be a condition for ribonuclease activity.

Structural features of plant chitinases and chitin-binding proteins.

Structural features of plant chitinases and chitin-binding proteins are discussed. Many of these proteins consist of multiple domains, of which the chitin-binding hevein domain is a predominant one. X-ray and NMR structures of representatives of the major classes of these proteins are available now, and are used to describe the structures of the other ones. Conserved positions of Cys residues can be taken as evidence for identically located disulfide bridges or cysteine residues. The current classification of chitinases is unsatisfactory and needs to be replaced by an evolutionarily more correct one. As the currently known three-dimensional structures of chitinases are those from barley and the rubber tree, Hevea brasiliensis, it is proposed to adopt the designation b-type (classes I, II and IV) and h-type (classes III and V) chitinases, respectively.