Charles Zelwer

Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2.5 Å resolution☆

Native methionyl-tRNA synthetase from Escherichia coli (a dimer of molecular weight 172,000) can be converted by mild proteolysis into a well-defined monomeric fragment of molecular weight 64,000. This fragment retains full specificity towards methionine and tRNAMet, and has unimpaired activity in both the activation and aminoacylation reactions. This paper describes the structure of the active fragment, as determined by an X-ray crystallographic study at 2.5 A resolution using five heavy-atom derivatives. The elongated molecule (90 A × 52 A × 44 A) contains several α-helices, which account for 43% of the residues. Three domains can be distinguished in the structure: (1) a central core beginning at the N-terminus, consisting of a five-stranded parallel pleated sheet with α-helices connecting the β-strands; (2) a second domain with less-ordered structure, inserted between the third and fourth strand of the central sheet; (3) a C-terminal domain, beginning after the fifth parallel strand, very rich in α-helices. These three domains are organized in a biglobular structure; one globule contains the first and the second domain (N-terminal globule), the other the third domain. The two globules, linked together by a single chain, are separated by a large cleft. The most salient feature of the structure is the presence, in the N-terminal domain, of a “nucleotide binding fold” similar to that first observed in dehydrogenases. This makes methionyl-tRNA synthetase, and possibly all aminoacyl-tRNA synthetases, a new member of this family of nucleotide binding proteins possessing the characteristic “Rossmann fold”.

Crystal structure of the phosphatidylethanolamine-binding protein from bovine brain: a novel structural class of phospholipid-binding proteins.

BACKGROUND Phosphatidylethanolamine-binding protein (PEBP) is a basic protein found in numerous tissues from a wide range of species. The screening of gene and protein data banks defines a family of PEBP-related proteins that are present in a variety of organisms, including Drosophila and inferior eukaryotes. PEBP binds to phosphatidylethanolamine and nucleotides in vitro, but its biological function in vivo is not yet known. The expression of PEBP and related proteins seems to be correlated with development and cell morphogenesis, however. To obtain new insights into the PEBP family and its potential functions, we initiated a crystallographic study of bovine brain PEPB. RESULTS The X-ray crystal structure of bovine brain PEBP has been solved using multiple isomorphous replacement methods, and refined to 1.84 A resolution. The structure displays a beta fold and exhibits one nonprolyl cis peptide bond. Analysis of cavities within the structure and sequence alignments were used to identify a putative ligand-binding site. This binding site is defined by residues of the C-terminal helix and the residues His85, Asp69, Gly109 and Tyr119. This site also corresponds to the binding site of phosphorylethanolamine, the polar head group of phosphatidylethanolamine. CONCLUSIONS This study shows that PEBP is not related to the G-protein family nor to known lipid-binding proteins, and therefore defines a novel structural family of phospholipid-binding proteins. The PEBP structure contains no internal hydrophobic pocket, as described for lipocalins or small phospholipid-transfer proteins. Nevertheless, in PEBP, a small cavity close to the protein surface has a high affinity for anions, such as phosphate and acetate, and also phosphorylethanolamine. We suggest that this cavity corresponds to the binding site of the polar head group of phosphatidylethanolamine.

Spatial distribution and hormonal regulation of gene products from methyl erythritol phosphate and monoterpene-secoiridoid pathways in Catharanthus roseus

The monoterpene indole alkaloids (MIAs) from Madagascar periwinkle (Catharanthus roseus) are secondary metabolites of high interest due to their therapeutical values. Secologanin, the monoterpenoid moiety incorporated into MIAs, is derived from the plastidial methyl-d-erythritol 4-phosphate (MEP) pathway. Here, we have cloned a cDNA encoding hydroxymethylbutenyl diphosphate synthase (HDS), a MEP pathway enzyme, and generated antibodies to investigate the distribution of transcripts and protein in MIA-producing aerial tissues. Consistent with our earlier work, transcripts for the genes encoding the so-called early steps in monoterpenoid biosynthesis (ESMB) enzymes (HDS, others MEP pathway enzymes and geraniol 10-hydroxylase) were preferentially co-localized to internal phloem associated parenchyma (IPAP) cells. By contrast, transcripts for the enzyme catalysing the last biosynthetic step to secologanin, secologanin synthase, were found in the epidermis. A coordinated response of ESMB genes was also observed in cell cultures stimulated to synthesise MIAs by hormone treatment, whereas no changes in SLS expression were detected under the same experimental conditions. Immunocytolabelling studies with the HDS-specific serum demonstrated the localisation of HDS to the plastid stroma and revealed that HDS proteins were most abundant in IPAP cells but could also be found in other cell types, including epidermal and mesophyll cells. Besides showing the existence of post-transcriptional mechanisms regulating the levels of HDS in C. roseus cells, our results support that intercellular translocation likely plays an important role during monoterpene-secoiridoid assembly.

Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase.

Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines such as 7,8-dihydro-8-oxoguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) from damaged DNA. Here, we report the crystal structure of the Fpg protein from Lactococcus lactis (LlFpg) bound to a carbocyclic FapydG (cFapydG)-containing DNA. The structure reveals that Fpg stabilizes the cFapydG nucleoside into an extrahelical conformation inside its substrate binding pocket. In contrast to the recognition of the 8-oxodG lesion, which is bound with the glycosidic bond in a syn conformation, the cFapydG lesion displays in the complex an anti conformation. Furthermore, Fpg establishes interactions with all the functional groups of the FapyG base lesion, which can be classified in two categories: (i) those specifying a purine-derived lesion (here a guanine) involved in the Watson-Crick face recognition of the lesion and probably contributing to an optimal orientation of the pyrimidine ring moiety in the binding pocket and (ii) those specifying the imidazole ring-opened moiety of FapyG and probably participating also in the rotameric selection of the FapydG nucleobase. These interactions involve strictly conserved Fpg residues and structural water molecules mediated interactions. The significant differences between the Fpg recognition modes of 8-oxodG and FapydG provide new insights into the Fpg substrate specificity.

Structure—activity relationships of methionyl-trna synthetase: graphics modelling and genetic engineering

Abstract The 3D structure of the methionyl-tRNA synthetase from E. coli has been investigated using X-ray analysis 1,2 at a resolution 1.8A. 90% of the molecule is now well defined and the zinc atom has been identified in a buried region of the molecule, close to the active site. At the same time, the refinement of the complex ATP-MetRS at 2.5 A has been carried out. The crystallographic R factor has been assigned a value of 25% at 2.5A with an overall temperature factor of 9A 2 and 22% when the individual temperature factors are refined. A Fourier difference map clearly reveals the electron density of the bound ATP, showing the phosphate groups deeply plunging into the active site. In parallel, the synthetase gene has been used to probe some of the enzyme structure-activity relationships. A series of 60 modified enzymes truncated at the C-terminus have been constructed in vitro and assayed for activity. In agreement with the graphics model, the results show that a minimum of 534 residues is necessary to sustain the aminoacylation reaction. A programme of site-directed mutagenesis is in progress: residues thought to be important for the catalytic activity, the metal coordination and tRNA interaction are being modified. Preliminary results are discussed in the light of the crystallographic model.

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA

Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3′ and 5′ sides by βδ-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5′–C4′–C3′ diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4′ leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.

A low-resolution model of crystalline methionyl-transfer RNA synthetase from Escherichia coli.

Abstract When submitted to a controlled proteolysis by trypsin, native methionyl-tRNA synthetase from Escherichia coli (a dimer of molecular weight 172,000) yields a well-defined fragment of molecular weight 64,000 composed of one single polypeptide chain. This fragment retains full specificity towards methionine and tRNA met , and has unimpaired activity in both the activation reaction and aminoacyl-tRNA formation. Crystals of this active fragment have been studied by X-ray crystallography and, using two isomorphous heavy-atom derivatives, a 4 A electron density map has been calculated. The molecule appears as an elongated ellipsoid of overall dimensions 90 A × 43 A × 43 A. It is clearly built of two parts separated by a large cleft. The volume of one of these “domains” is approximately twice that of the other; these results are consistent with our present knowledge of the chemistry of the protein.

Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family

Yhr049w/FSH1 was recently identified in a combined computational and experimental proteomics analysis for the detection of active serine hydrolases in yeast. This analysis suggested that FSH1 might be a serine‐type hydrolase belonging to the broad functional αβ‐hydrolase superfamily. In order to get insight into the molecular function of this gene, it was targeted in our yeast structural genomics project. The crystal structure of the protein confirms that it contains a Ser/His/Asp catalytic triad that is part of a minimal α/β‐hydrolase fold. The architecture of the putative active site and analogies with other protein structures suggest that FSH1 may be an esterase. This finding was further strengthened by the unexpected presence of a compound covalently bound to the catalytic serine in the active site. Apparently, the enzyme was trapped with a reactive compound during the purification process.

Synthesis of an Enantiomerically Pure Carbocyclic DNA Abasic Site Analogue

Abstract A short synthetic route to an appropriately derivatized carbocyclic analogue of abasic site residues of DNA is proposed.