Putative Substrate-binding Domain Research Articles

The structural basis of tRNA recognition by arginyl-tRNA-protein transferase

Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.

Crystal structures of an archaeal chitinase ChiD and its ligand complexes.

Chitinase D (designated as Pc-ChiD) was found in a hyperthermophilic archaeon, Pyrococcus chitonophagus (previously described as Thermococcus chitonophagus), that was isolated from media containing only chitin as carbon source. Pc-ChiD displays chitinase activity and is thermostable at temperatures up to 95°C, suggesting its potential for industrial use. Pc-ChiD has a secretion signal peptide and two chitin-binding domains (ChBDs) in the N-terminal domain. However, the C-terminal domain shares no sequence similarity with previously identified saccharide-degrading enzymes and does not contain the DXDXE motif conserved in the glycoside hydrolase (GH) 18 family chitinases. To elucidate its overall structure and reaction mechanism, we determined the first crystal structures of Pc-ChiD, both in the ligand-free form and in complexes with substrates. Structure analyses revealed that the C-terminal domain of Pc-ChiD, Pc-ChiD(ΔBD), consists of a third putative substrate-binding domain, which cannot be predicted from the amino acid sequence, and a catalytic domain structurally similar to that found in not the GH18 family but the GH23 family. Based on the similarity with GH23 family chitinase, the catalytic residues of Pc-ChiD were predicted and confirmed by mutagenesis analyses. Moreover, the specific C-terminal 100 residues of Pc-ChiD are important to fix the putative substrate-binding domain next to the catalytic domain, contributing to the structure stability as well as the long chitin chain binding. Our findings reveal the structure of a unique archaeal chitinase that is distinct from previously known members of the GH23 family.

Crystal Structure of the Substrate-Binding Domain from Listeria monocytogenes Bile-Resistance Determinant BilE

BilE has been reported as a bile resistance determinant that plays an important role in colonization of the gastrointestinal tract by Listeria monocytogenes, the causative agent of listeriosis. The mechanism(s) by which BilE mediates bile resistance are unknown. BilE shares significant sequence similarity with ATP-binding cassette (ABC) importers that contribute to virulence and stress responses by importing quaternary ammonium compounds that act as compatible solutes. Assays using related compounds have failed to demonstrate transport mediated by BilE. The putative substrate-binding domain (SBD) of BilE was expressed in isolation and the crystal structure solved at 1.5 Å. Although the overall fold is characteristic of SBDs, the binding site varies considerably relative to the well-characterized homologs ProX from Archaeoglobus fulgidus and OpuBC and OpuCC from Bacillus subtilis. This suggests that BilE may bind an as-yet unknown ligand. Elucidation of the natural substrate of BilE could reveal a novel bile resistance mechanism.

The Large Hsp70 Grp170 Binds to Unfolded Protein Substrates in Vivo with a Regulation Distinct from Conventional Hsp70s

The Hsp70 superfamily is a ubiquitous chaperone class that includes conventional and large Hsp70s. BiP is the only conventional Hsp70 in the endoplasmic reticulum (ER) whose functions include: assisting protein folding, targeting misfolded proteins for degradation, and regulating the transducers of the unfolded protein response. The ER also possesses a single large Hsp70, the glucose-regulated protein of 170 kDa (Grp170). Like BiP it is an essential protein, but its cellular functions are not well understood. Here we show that Grp170 can bind directly to a variety of incompletely folded protein substrates in the ER, and as expected for a bona fide chaperone, it does not interact with folded secretory proteins. Our data demonstrate that Grp170 and BiP associate with similar molecular forms of two substrate proteins, but while BiP is released from unfolded substrates in the presence of ATP, Grp170 remains bound. In comparison to conventional Hsp70s, the large Hsp70s possess two unique structural features: an extended C-terminal α-helical domain and an unstructured loop in the putative substrate binding domain with an unknown function. We find that in the absence of the α-helical domain the interaction of Grp170 with substrates is reduced. In striking contrast, deletion of the unstructured loop results in increased binding to substrates, suggesting the presence of unique intramolecular mechanisms of control for the chaperone functions of large Hsp70s.

FAD-Binding Site and NADP Reactivity in Human Renalase: A New Enzyme Involved in Blood Pressure Regulation

Renalase is a recently discovered flavoprotein that regulates blood pressure, regulates sodium and phosphate excretion, and displays cardioprotectant action through a mechanism that is barely understood to date. It has been proposed to act as a catecholamine-degrading enzyme, via either O 2-dependent or NADH-dependent mechanisms. Here we report the renalase crystal structure at 2.5 Å resolution together with new data on its interaction with nicotinamide dinucleotides. Renalase adopts the p-hydroxybenzoate hydroxylase fold topology, comprising a Rossmann-fold-based flavin adenine dinucleotide (FAD)-binding domain and a putative substrate-binding domain, the latter of which contains a five-stranded anti-parallel β-sheet. A large cavity (228 Å 3), facing the flavin ring, presumably represents the active site. Compared to monoamine oxidase or polyamine oxidase, the renalase active site is fully solvent exposed and lacks an ‘aromatic cage’ for binding the substrate amino group. Renalase has an extremely low diaphorase activity, displaying lower k cat but higher k cat/ K m for NADH compared to NADPH. Moreover, its FAD prosthetic group becomes slowly reduced when it is incubated with NADPH under anaerobiosis, and binds NAD + or NADP + with K d values of ca 2 mM. The absence of a recognizable NADP-binding site in the protein structure and its poor affinity for, and poor reactivity towards, NADH and NADPH suggest that these are not physiological ligands of renalase. Although our study does not answer the question on the catalytic activity of renalase, it provides a firm framework for testing hypotheses on the molecular mechanism of its action.

Structure of the N-terminal fragment of Escherichia coli Lon protease.

The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal alpha-helix. The structure of the first subdomain (residues 1-117), which consists mostly of beta-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.

Insights into Heterocyclization from Two Highly Similar Enzymes

The cyanobactin biosynthetic pathways pat and tru, isolated from metagenomes of marine animals, lead to diverse natural products containing heterocycles derived from Cys, Ser, and Thr. Previous work has shown that PatD and TruD are extremely broad-substrate heterocyclase enzymes. These enzymes are virtually identical in their N-terminal putative catalytic domains, but only approximately 77% identical in their C-terminal putative substrate-binding domains. Here, we show that these differences allow the enzymes to control regioselectivity of posttranslational modifications, helping to control product chemistry in this hypervariable family of marine natural products.

Genetic and biochemical characterization of poly 3-hydroxybutyrate depolymerase from Diaphorobacter sp. PCA039

Diaphorobacter sp. PCA039 secreted a polyhydroxybutyrate (PHB) depolymerase into the culture supernatant when it was cultivated on poly 3-PHB or poly 3-hydroxybutyrate-co-3-hydroxyvalerate [PHB(V)] as the sole carbon source. A PHB(V) depolymerase-encoding gene (phaZd) was cloned by construction of a Fosmid genomic library and degenerate primer screening, and overexpressed in Escherichia coli BL21 (DE3). The nucleotide sequence analysis of this gene revealed that it encoded a protein of 507 amino acids with a calculated molecular mass of 52,247 Da. The deduced amino acid sequence had 70% identity to that of the PHB depolymerase from Commonas strains and consisted a conserved lipase box sequence (G-L-S*40- S-G) in the N-terminal region. Analysis suggested that the protein contains a catalytic domain, a fibronectin type III module as a linker, and a putative substrate-binding domain. Furthermore, transcription detection of the phaZd product indicated that PhaZd is a very important degrading enzyme when PHB(V) served as sole carbon source. Further depolymerase enzyme assay data showed that the optimum temperature and pH for the purified enzyme were 40°C and 8.0, respectively.

Crystal structure of SopA, a Salmonella effector protein mimicking a eukaryotic ubiquitin ligase

Bacterial pathogens deliver virulence proteins into host cells to facilitate entry and survival. Salmonella SopA functions as an E3 ligase to manipulate the host proinflammatory response. Here we report the crystal structure of SopA in two conformations. Although it has little sequence similarity to eukaryotic HECT-domain E3s, the C-terminal half of SopA has a bilobal architecture that is reminiscent of the N- and C-lobe arrangement of HECT domains. The SopA structure also contains a putative substrate-binding domain located near the E2-binding site. The two structures of SopA differ in the relative orientations of the C lobe, indicating that SopA possesses the conformational flexibility essential for HECT E3 function. These results suggest that SopA is a unique HECT E3 ligase evolved from the coevolutionary selective pressure at the bacterium-host interface.

Sphingolipid biosynthesis in pathogenic fungi: Identification and characterization of the 3-ketosphinganine reductase activity of Candida albicans and Aspergillus fumigatus

An early step in sphingolipid biosynthesis, the reduction of 3-ketosphinganine, is catalyzed in the yeast Saccharomyces cerevisiae by Tsc10p ( TSC10 ( YBR265W)). We have identified orthologs of TSC10 in two clinically important fungal pathogens, Candida albicans and Aspergillus fumigatus. The translated sequences of the putative C. albicans ortholog, KSR1 (orf6.5112), and the putative A. fumigatus ortholog, ksrA, show significant homology to the yeast protein. All three proteins contain the signature motifs of NAD(P)H-dependent oxidoreductases in the short-chain dehydrogenase/reductase family and a conserved putative substrate-binding domain. Despite being essential in S. cerevisiae, we demonstrate that the C. albicans ortholog, KSR1, is not required for cell viability. However, ksr1 null mutants produce lower levels of inositolphosphorylceramides, are significantly more sensitive than the wildtype to an inhibitor of a subsequent step in sphingolipid biosynthesis, and are defective for the transition from yeast to filamentous growth, a key virulence determinant. Recombinant, purified Ksr1p and KsrA can carry out the reduction of 3-ketosphinganine in an NADPH-dependent manner. Molecular modeling of Ksr1p with bound substrates suggests that a significant portion of the aliphatic chain of 3-ketosphinganine protrudes from the enzyme. Guided by this molecular model, we developed shorter, water-soluble derivatives of 3-ketosphinganine that are substrates for 3-ketosphinganine reductase.

Site-Directed Mutagenesis and Use of Bile Acid−MTS Conjugates to Probe the Role of Cysteines in the Human Apical Sodium-Dependent Bile Acid Transporter (SLC10A2)

The residues involved in substrate interaction of the human apical sodium-dependent bile acid transporter (hASBT, SLC10A2) remain undefined. Biochemical modification of conserved cysteine residues has suggested their direct involvement in hASBT function. In the present study, we developed novel methanethiosulfonyl (MTS)-bile salt derivatives and describe their reactivity toward hASBT and its mutants. Endogenous Cys residues were subjected to Ala/Thr scanning mutagenesis and subsequent exposure to affinity inactivators. We show that C51A/T, C105A/T, C144A, and C255A/T are loss-of-function mutations. Additionally, C74A/T cell surface expression was abolished suggesting a role in protein folding and/or trafficking. C270A remained largely unaffected in the presence of 1.0 mM polar and charged MTS reagents (MTSEA, MTSES, and MTSET) and retained function similar to wt-hASBT control. However, in the presence of synthetic cholyl- and chenodeoxycholyl-MTS analogues, C270A displayed a significant decrease in K(T) and J(max). Our findings demonstrate that Cys270 is a highly accessible extracellular residue susceptible to thiol modification in its native form that remains largely unaffected upon mutation to Ala. Consequently, C270A provides an ideal scaffold for cysteine scanning mutagenesis studies. Furthermore, the substantial decrease in ligand affinity and maximal transport capacity of C270A suggest that C270 may potentially impact, although not critically, a putative substrate binding domain of hASBT. Overall, bile acid-MTS conjugates can serve as novel and powerful tools to probe the role of endogenous as well as engineered Cys residues and, ultimately, aid in defining their role in the bile acid binding region(s) of hASBT.

Structural Characterization and Comparative Phylogenetic Analysis of Escherichia coli HemK, a Protein (N5)-glutamine Methyltransferase

Protein glutamine methylation at GGQ sites of protein chain release factors plays a pivotal role in the termination of translation. We report here the crystal structure of the Escherichia coli HemK protein (N5)-glutamine methyltransferase (MTase) in a binary complex with the methyl-donor product S-adenosyl-l-homocysteine (AdoHcy). HemK contains two domains: a putative substrate binding domain at the N terminus consisting of a five helix bundle and a seven-stranded catalytic domain at the C terminus that harbors the binding site for AdoHcy. The two domains are linked by a β-hairpin. Structure-guided sequence analysis of the HemK family revealed 11 invariant residues functioning in methyl-donor binding and catalysis of methyl transfer. The putative substrate-binding domains of HemK from E.coli and Thermotoga maritima are structurally similar, despite the fact that they share very little sequence similarity. When the two proteins are aligned structurally, the helical N-terminal domain is subject to approximately 10° of hinge movement relative to the C-terminal domain. The apparent hinge mobility of the two domains may reflect functional importance during the reaction cycle. Comparative phylogenetic analysis of the hemK gene and its frequent neighbor gene, prfA, which encodes a major substrate, provides evidence for several examples of lateral gene transfer.

The Crystal Structure of the UvsW Helicase from Bacteriophage T4

In bacteriophage T4, the WXY system repairs DNA damage by a process that involves homologous recombination. This system comprises three proteins, the RecA-like recombination protein UvsX, a recombination mediator protein UvsY, and a helicase UvsW. Here we report the 2.0 Å resolution crystal structure of the N-terminal two domains of the UvsW helicase (UvsWNF; residues 1–282). The structure reveals a typical helicase RecA-like domain linked to a small N-terminal α/β domain that likely binds the nucleic acid substrate. The missing C-terminal portion of UvsW almost certainly corresponds to the second RecA-like domain typically found in monomeric helicases. The putative substrate binding domain is unique within the known helicase structures, and it resembles the novel “double-wing” DNA binding domain from the phage T4 MotA transcription factor that mediates the expression of T4 middle genes. The functional implications of this homology for the role of UvsW in T4 DNA metabolism are discussed.

Isolation and characterization of the UGT2B28 cDNA encoding a novel human steroid conjugating UDP-glucuronosyltransferase.

UDP-glucuronosyltransferase (UGT) enzymes belonging to the UGT2B subfamily catalyze the transfer of glucuronic acid to a large number of endogenous compounds, particularly steroids, to facilitate their elimination from target cells. A novel human UGT2B cDNA of 1666 bp was isolated and encodes a 529-amino acid protein named UGT2B28 type I. Glucuronidation assays demonstrated that UGT2B28 type I catalyzes the conjugation of endogenous and exogenous compounds. The tissue distribution of UGT2B28 revealed the expression of the type I transcript in the liver, breast, and LNCaP cells. Two other UGT2B cDNAs were isolated, and sequence analysis led to the identification of two truncated UGT2B28 species. UGT2B28 type II differs from type I by a deletion of 308 bp in the cofactor binding domain, whereas UGT2B28 type III lacks 351 bp in the putative substrate binding domain. All UGT2B28 isoforms are encoded by a single UGT2B28 gene which has a genomic organization similar to that of the other UGT2B genes characterized thus far. Although no substrates could be identified for the shorter isoforms, the three subtypes were shown to be located in the endoplasmic reticulum and the perinuclear membrane, demonstrating that the missing domains are not required for the subcellular localization of these UGT2B proteins. However, all the domains remain necessary for observing glucuronidation activity. The expression of UGT2B28 type I in the breast and liver suggests a role of this enzyme in the androgen and estrogen metabolism in these tissues.

Structural heterogeneity at the UDP-glucuronosyltransferase 1 locus: functional consequences of three novel missense mutations in the human UGT1A7 gene.

One of the most important mechanisms involved in host defense against xenobiotic chemicals and endogenous toxins is the glucuronidation catalysed by UDP-glucuronosyltransferase enzymes (UGT). The role of genetic factors in determining variable rates of glucuronidation is not well understood, but phenotypic evidence in support of such variation has been reported. In the present study, six single nucleotide polymorphisms were discovered in the first exon of the UGT1A7 gene, which codes for the putative substrate-binding domain, revealing a high structural heterogeneity at the UGT1 gene locus. The new UGT1A7 proteins differ in their primary structure at amino acid positions 129, 131 and 208, creating four distinct UGT1A7 allelic variants in the human population: UGT1A7*1 (N129 R131 W208), *2 (K129 K131 W208), *3 (K129 K131 R208), and *4 (N129 R131 R208). In functional studies, HEK cells stably transfected to express the four allelic UGT1A7 variants exhibited significant differences in catalytic activity towards 3-, 7-, and 9-hydroxy-benzo(a)pyrene. UGT1A7*3 exhibited a 5.8-fold lower relative Vmax compared to wild-type *1, whereas *2 and *4 had a 2.6- and 2.8-fold lower relative Vmax than *1, respectively, suggesting that these mutations confer slow glucuronidation phenotype. Kinetic characterization suggested that these differences were primarily attributable to altered Vmax. Additionally, it suggested that each amino acid substitutions can independently affect the UGT1A7 catalytic activity, and that their effects are additive. The expression pattern of UGT1A7 studied herein and its catalytic activity profile suggest a possible role of UGT1A7 in the detoxification and elimination of carcinogenic products in lung. A population study demonstrated that a considerable proportion of the population (15.3%) was found homozygous for the low activity allele containing all three missense mutations, UGT1A7*3. These findings suggest that further studies are needed to investigate the impact of the low UGT1A7 conjugator genotype on individual susceptibility to chemical-induced diseases and responses to therapeutic drugs.

Structure of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum as studied by electron tomography

Valosine-containing protein-like ATPase from Thermoplasma acidophilum is a member of the superfamily of ATPases associated with a diversity of cellular activities and is closely related to CDC48 from yeast and p97 from higher eukaryotes and more distantly to N-ethylmaleimide-sensitive fusion protein. We have used electron tomography to obtain low-resolution (2–2.5 nm) three-dimensional maps of both the whole 500 kDa complex and the N-terminally truncated valosine-containing protein-like ATPase from T. acidophilum complex lacking the putative substrate binding domain.

Cloning and characterization of the polyhydroxybutyrate depolymerase gene of Pseudomonas stutzeri and analysis of the function of substrate-binding domains.

The extracellular polyhydroxybutyrate (PHB) depolymerase gene (phaZPst) of Pseudomonas stutzeri was cloned and sequenced. phaZPst was composed of 1,728 bp encoding a protein of 576 amino acids. Analyses of the N-terminal amino acid sequence and the matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrum of the purified enzyme showed that the mature enzyme consisted of 538 amino acids with a deduced molecular mass of 57,506 Da. Analysis of the deduced amino acid sequence of the protein revealed a domain structure containing a catalytic domain, putative linker region, and two putative substrate-binding domains (SBDI and SBDII). The putative linker region was similar to the repeating units of the cadherin-like domain of chitinase A from Vibrio harveyi and chitinase B from Clostridium paraputrificum. The binding characteristics of SBDs to poly([R]-3-hydroxybutyrate) [P(3HB)] and chitin granules were characterized by using fusion proteins of SBDs with glutathione S-transferase (GST). These GST fusion proteins with SBDII and SBDI showed binding activity toward P(3HB) granules but did not bind on chitin granules. It has been suggested that the SBDs of the depolymerase interact specifically with the surface of P(3HB). In addition, a kinetic analysis for the enzymatic hydrolysis of 3-hydroxybutyrate oligomers of various sizes has suggested that the catalytic domain of the enzyme recognizes at least two monomeric units as substrates.

Biochemical and molecular characterization of the polyhydroxybutyrate depolymerase of Comamonas acidovorans YM1609, isolated from freshwater.

Comamonas acidovorans YM1609 secreted a polyhydroxybutyrate (PHB) depolymerase into the culture supernatant when it was cultivated on poly(3-hydroxybutyrate) [P(3HB)] or poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [P(3HB-co-3HV)] as the sole carbon source. The PHB depolymerase was purified from culture supernatant of C. acidovorans by two chromatographic methods, and its molecular mass was determined as 45,000 Da by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The enzyme was stable at temperatures below 37 degrees C and at pH values of 6 to 10, and its activity was inhibited by diisopropyl fluorophosphonate. The liquid chromatography analysis of water-soluble products revealed that the primary product of enzymatic hydrolysis of P(3HB) was a dimer of 3-hydroxybutyric acid. Kinetics of enzymatic hydrolysis of P(3HB) film were studied. In addition, a gene encoding the PHB depolymerase was cloned from the C. acidovorans genomic library. The nucleotide sequence of this gene was found to encode a protein of 494 amino acids (M(r), 51,018 Da). Furthermore, by analysis of the N-terminal amino acid sequence of the purified enzyme, the molecular mass of the mature enzyme was calculated to be 48,628 Da. Analysis of the deduced amino acid sequence suggested a domain structure of the protein containing a catalytic domain, fibronectin type III module as linker, and a putative substrate-binding domain. Electron microscopic visualization of the mixture of P(3HB) single crystals and a fusion protein of putative substrate-binding domain with glutathione S-transferase demonstrated that the fusion protein adsorbed strongly and homogeneously to the surfaces of P(3HB) single crystals.

Cloning of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122, and characterization of its gene product

A DNA fragment that carries the gene coding for poly(3-hydroxybutyrate) (PHB) depolymerase was cloned from the chromosomal DNA of Alcaligenes faecalis AE122 isolated from seawater. The open reading frame encoding the precursor of the PHB depolymerase was 1905 base pairs (bp) long, corresponding to a protein of 635 amino acid residues ( M r=65 208). The promoter site, which could be recognized by Escherichia coli RNA polymerase, was upstream from the gene, and the sequence adhering to the ribosome-binding sequence was found in front of the gene. The deduced amino acid sequence agreed with the N-terminal amino acid sequence of the purified PHB depolymerase from amino acid 28 onwards. Analysis of the deduced amino acid sequence revealed the domain structure of the protein; a signal peptide of 27 amino acids long was followed by a catalytic domain of about 400 amino acids, a fibronectin type III module sequence, and a putative substrate binding domain. The molecular mass (62 526) of the mature protein deduced from the nucleotide sequence was significantly lower than the value (95 kDa) estimated on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, but coincided well with the value (62 426) estimated from matrix-assisted laser desorption ionization mass spectra. By comparison of the primary structure with those of other PHB depolymerases, the substrate binding domain was found to consist of two domains, PHB-specific and poly(3-hydroxyvalerate)-specific ones, connected by a linker region. The PHB depolymerase gene was expressed in Escherichia coli under the control of the tac promoter. The enzyme expressed in E. coli was purified from culture broth and showed the same catalytic properties as the enzyme from A. faecalis. © 1997 Elsevier Science B.V. All rights reserved.

Effects of random mutagenesis in a putative substrate-binding domain of geranylgeranyl diphosphate synthase upon intermediate formation and substrate specificity.

Archaeal geranylgeranyl diphosphate (GGPP) synthase catalyzes the consecutive condensation of isopentenyl diphosphate (IPP) with allylic diphosphates to produce GGPP with significant amounts of intermediates. To obtain information about the amino acids involved in the condensation and the release of intermediates, we randomly mutagenized two proximal regions, I and II, of the Sulfolobus acidocaldarius GGPP synthase gene and created two degenerate libraries, I and II, respectively. Regions I and II correspond to amino acid residues 170-173 and 166-168, respectively. The prenyltransferase activities of about 200 clones were analyzed using the in vivo red-white system and the conventional in vitro assay. Although, in library I, no mutated enzymes that failed to catalyze the formation of GGPP were found, as assayed with the red-white system, almost all the mutated enzymes exhibited weak GGPP synthesis activity, and many produced large amounts of intermediates. The formation of intermediates increased as the concentration of IPP was decreased or as the concentration of the allylic substrate was increased. These phenomena can be regarded as a reflection of the increased K(m) for IPP and the decreased affinity for products including intermediates. On the other hand, no mutants from library II showed such changes. These results suggest that the region from 170 to 173 is concerned in the recognition of both IPP and allylic diphosphates, and that the change in responsiveness to prenyl diphosphates causes a change in intermediate formation.