Sequencing synthases comparison

The amino acid sequence similarities of all 36 PHA synthases were pairwise revealed, and the results of this comparison are compiled in Table 2. The data correspond well with phylogenetic tree shown in Fig. 1, and the similarities va-... 

Fig. 2a-d. Multiple alignment of primary structures from 36 PHA synthases. A comparison of amino acid sequences derived from PH A synthase genes is shown. Amino acids are specified by the standard one-letter abbreviations. The consensus sequence represents amino acid residues (shaded) which are present in at least 50% of the PHA synthases. Highly conserved amino acids, which are present in at least 70% of the PHA synthases, are additionally underlined in the consensus sequence and the eight amino acid residues, which are present in all PHA synthases, are indicated as bold letters. See Table 1 for references... 

The peptide sequences obtained for codeinone reductase aligned well with the amino acid sequences for 6 -deoxychalcone synthase (chalcone reductase) from alfalfa, Glycerrhiza, and soybean. Knowledge of the relative positions of the peptides allowed for a quick RT-PCR based isolation of cDNAs encoding codeinone reductase from P. somniferum. The codeinone reductase isoforms are 53 % identical to chalcone reductase from soybean.25 By sequence comparison, both codeinone reductase and chalcone reductase belong to the aldo/keto reductase family, a group of structurally and functionally related NADPH-dependent oxidoreductases, and thereby possibly arise from primary metabolism. Six alleles encoding codeinone... 

Figure 12.5 A. Comparison of the CHS monomer (left) and P-ketoacyl synthase monomer (right). The structurally conserved secondary structure of each monomer s upper domain is colored in blue (a-helix) and gold (P-strand). Portions of each protein monomer forming the dimer interface are colored purple. The side-chains of the catalytic residues of CHS (Cysl64, His303, Asn336) and P-ketoacyl synthase (Cysl63, His303, His340) are shown. B. Sequence conservation of the catalytic residues of CHS, 2-PS, p-ketoacyl synthase (FAS II), and the ketosynthase modules of 6-deoxyerythronolide B synthase (DEBS), actinorhodin synthase (ActI) and tetracenomycin synthase (TcmK). The catalytic residues are in red.

Fig. 11.4 Sequence comparison of Arabidopsis geranyllinalool synthase with other Arabidopsis TPS and putative or characterized linalool and geranyllinalool synthases from Clarkia, Medicago, poplar and grape. A neighbor-joining tree generated from an amino acid sequence alignment (QustalX) of 13 TPS proteins is shown. Numbers are bootstrap values higher than 800 out of 1,000 replicates. TPS proteins belong to different families as indicated by letters. V. vinifera putative GES, Acc. 002268557 P. trichocarpa putative GES, Acc. 002305640...

Much of the information on ANS has come not from studies on enzyme extracts but from analysis of DNA sequences and recombinant proteins. Sequences for the ANS were first isolated using transposon generated mutant lines of A. majus and Z. mays They encoded proteins of 40 to 41 kDa that were found to have similarity to 20GDs, during a study on a nonflavonoid enzyme. This sequence-based identification was confirmed by the in vitro assay of the recombinant Perilla frutescens protein, and subsequent assays on recombinant ANS from a range of species that confirmed the requirement for Fe, 20G, and ascorbate. Sequence comparisons show that ANS is more closely related to flavonol synthase (FLS), another 20GD, than to F3H. 

Most of the compounds shown in Figure 22-4 are derived from the C15 famesyl diphosphate. There are more than 300 known cyclic structures among these sesquiterpenes, and many sesquiterpene synthases have been characterized.91/91a Aristolochene is formed by the action of a 38-kDa cyclase that has been isolated from species of Penicillium and Aspergillus,92"4 Notice that the synthesis must involve two cyclization steps and migration of a methyl group. Three-dimensional structures are known for at least two terpene synthases,95 96 and comparison of gene sequences suggests that many others have similar structures. 

Jorgensen RA, Cluster PD, English J, Que Q, Napoli CA (1996) Chalcone synthase cosuppression phenotypes in petunia flowers comparison of sense vs antisense constructs and single-copy vs complex T-DNA sequences. Plant Mol Biol 31 957-973... 

Independent of the actual mechanism, functional divergence between two proteins with a common ancestor is exemplified in the /la-barrel structures of N-(phosphor-ibosyl-formimino)-aminoimidazole-carboxamide ribonucleotide isomerase (HisA) and imidazole glycerol phosphate synthase (HisF) of the histidine biosynthetic pathway [16]. The hypothesis of a common origin of the two enzymes was formulated based on sequence comparison [17] and has recently found support by the identification of extensive structural similarities [18],... 

Chen, A., Kroon, P.A. and Poulter, C.D. (1994) Isoprenyl diphosphate synthases protein sequence comparisons, a phylogenetic tree and predictions of secondary structure. Protein Sci., 3, 600-7. 

FIGURE 2 Amino acid conservation between acetolactate synthase genes. The numbers indicate amino acid residues. The first bar represents a comparison of the deduced amino acid sequences of ALS from tobacco and Arabidopsis-, the second bar represents a comparison between the amino acid sequences of the three E. coli ALS isozymes. Regions of conservation are shown in white. 

For instance, terpene cyclases are known to catalyze the conversion of oligomeric isoprenoid pyrophosphate substrates to polycyclic hydrocarbon products. Sequence comparisons of terpene cyclases with different known specificity can allow them to be classified into monoterpene, sesquiterpene, and diterpene synthases, which utilize the 10-carbon substrate geranyl pyrophosphate, the 15-carbon substrate famesyl pyrophosphate, and the 20-carbon substrate geranyl-geranyl pyrophosphate, respectively, on the basis of sequence criteria. 

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