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1.
The available amino acid sequences of the α-amylase family (glycosyl hydrolase family 13) were searched to identify their
domain B, a distinct domain that protrudes from the regular catalytic (β/α)8-barrel between the strand β3 and the helix α3. The isolated domain B sequences were inspected visually and also analyzed
by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional
structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different
forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in
the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an α-helix succeeded by a three-stranded antiparallel β-sheet. These enzymes are α-glucosidase,
cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few α-amylases. Domain B
of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable
similarity with (β/α)8-barrel elements throughout the entire sequence of enzymes from the oligo-1,6-glucosidase group. The transport proteins, in
turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only
parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the α-amylase family.
Received: 4 December 1996 / Accepted: 13 March 1997 相似文献
2.
Fungi have evolved a unique α-aminoadipate pathway for lysine biosynthesis. The fungal-specific enzyme homoaconitate hydratase
from this pathway is moderately similar to the aconitase-family proteins from a diverse array of taxonomic groups, which have
varying modes of obtaining lysine. We have used the similarity of homoaconitate hydratase to isopropylmalate isomerase (serving
in leucine biosynthesis), aconitase (from the tricarboxylic acid cycle), and iron-responsive element binding proteins (cytosolic
aconitase) from fungi and other eukaryotes, eubacteria, and archaea to evaluate possible evolutionary scenarios for the origin
of this pathway. Refined sequence alignments show that aconitase active site residues are highly conserved in each of the
enzymes, and intervening sequence sites are quite dissimilar. This pattern suggests strong purifying selection has acted to
preserve the aconitase active site residues for a common catalytic mechanism; numerous other substitutions occur due to adaptive
evolution or simply lack of functional constraint. We hypothesize that the similarities are the remnants of an ancestral gene
duplication, which may not have occurred within the fungal lineage. Maximum likelihood, neighbor joining, and maximum parsimony
phylogenetic comparisons show that the α-aminoadipate pathway enzyme is an outgroup to all aconitase family proteins for which
sequence is currently available.
Received: 7 October 1997 相似文献
3.
The amino acid sequences of 22 α-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the
evolutionary relationships between the archaeal α-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary
distance trees were constructed: (i) the first one based on the alignment of extracted best-conserved sequence regions (58
residues) comprising β2, β3, β4, β5, β7, and β8 strand segments of the catalytic (α/β)8-barrel and a short conserved stretch in domain B protruding out of the barrel in the β3 →α3 loop, and (ii) the second one
based on the alignment of the substantial continuous part of the (α/β)8-barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal α-amylases, both trees compared
brought, in fact, the same results; i.e., all family 13 α-amylases from domain Archaea were clustered with barley pI isozymes,
which represent all plant α-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic α-amylases, respectively, seem to be the further closest relatives to archaeal α-amylases.
This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these α-amylases,
especially in the best-conserved sequence regions. Since the results for α-amylases belonging to all three domains (Eucarya,
Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is proposed that the investigated conserved sequence
regions may indeed constitute the ``sequence fingerprints' of a given α-amylase.
Received: 3 June 1998 / Accepted: 20 August 1998 相似文献
4.
Warwicker J 《Planta》2001,212(3):343-347
Sequence comparison indicates that auxin-binding protein 1 (ABP1) belongs to a family of proteins with the core β-barrel
structure of the vicilins. Previous modelling within this family correctly predicted metal-ion binding and oligomeric properties
of oxalate oxidase. ABP1 also contains a putative metal-ion-binding cluster of amino acids, adjacent to a tryptophan side
chain, leading to a proposed auxin-binding site that incorporates metal-ion interaction with the auxin carboxylate. Modelling
implicates W44 (Zea mays ABP1) in auxin binding, rather than W136 or W151. Reduced sequence similarity for the C-terminal region prevents model building.
It is proposed that one of these C-terminal tryptophans, along with a neighbouring negatively charged side chain, occupies
the binding pocket in the absence of auxin, thereby linking auxin binding to conformational change and C-terminal involvement
in signalling.
Received: 10 December 1999 / Accepted: 4 August 2000 相似文献
5.
Christine P. Piotte Airlie K. Hunter Craig J. Marshall Murray R. Grigor 《Journal of molecular evolution》1998,46(3):361-369
Three proteins have been identified in the milk of the common brush tail possum, Trichosurus vulpecula that from sequence analysis are members of the lipocalin family. They include β-lactoglobulin, which appears to have two
forms; a homologue to the late-lactation protein found in tammar, Macropus eugenii; milk; and a novel protein termed trichosurin. Whereas β-lactoglobulin and trichosurin are both expressed throughout lactation, the late-lactation protein is not detected
in samples taken before days 100–110 of lactation. The cDNAs encoding each of these proteins have been isolated from cDNA
libraries prepared using possum mammary mRNA and sequenced. Phylogenetic analysis showed that the T. vulpeculaβ-lactoglobulin, along with two other macropod β-lactoglobulins, forms a subclass of β-lactoglobulins distinct from those
for eutherian mammals; both marsupial late-lactation proteins appear to have similarities to a family of odorant-binding proteins,
whereas trichosurin has similarities to the major urinary proteins of rodents.
Received: 28 October 1996 / Accepted: 19 May 1997 相似文献
6.
A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA
gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly
within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is
likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA
gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely
to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
Received: 24 November 1997 / Accepted: 14 September 1998 相似文献
7.
Microbial Relatives of Seed Storage Proteins: Conservation of Motifs in a Functionally Diverse Superfamily of Enzymes 总被引:1,自引:0,他引:1
Plant storage proteins comprise a major part of the human diet. Sequence analysis has revealed that these proteins probably
share a common ancestor with a fungal oxalate decarboxylase and/or related bacterial genes. Additionally, all these proteins
share a central core sequence with several other functionally diverse enzymes and binding proteins, many of which are associated
with synthesis of the extracellular matrix during sporulation/encystment. A possible prokaryotic relative of this sequence
is a bacterial protein (SASP) known to bind to DNA and thereby protect spores from extreme environmental conditions. This
ability to maintain cell viability during periods of dehydration in spores and seeds may relate to absolute conservation of
residues involved in structure determination.
Received: 25 April 1997 / Accepted: 29 July 1997 相似文献
8.
The predicted secondary structure of both subunits of bacterial luciferase is in accordance with a regular 8-fold α/β-barrel structure. The 3D profile1,2 confirmed that luciferase subunits are compatible with the α/β-barrel despite the absence of sequence similarity with any α/β-barrel protein. The three-dimensional structure of 260 residues of the α-chain of luciferase was modeled from coordinates of glycolate oxidase and then energy minimized. The model obtained satisfies the criteria for the structure of a globular protein and is in accordance with known experimental data. From the model it is possible to predict active site residues involved in binding and catalysis. These predictions, and thus also the model, can be tested by protein engineering experiments. © 1995 Wiley-Liss, Inc. 相似文献
9.
Benoit Cousineau Fabrice Leclerc Robert Cedergren 《Journal of molecular evolution》1997,45(6):661-670
Sequence similarity has given rise to the proposal that IF-2, EF-G, and EF-Tu are related through a common ancestor. We evaluate
this proposition and whether the relationship can be extended to other factors of protein synthesis. Analysis of amino acid
sequence similarity gives statistical support for an evolutionary affiliation among IF-1, IF-2, IF-3, EF-Tu, EF-Ts, and EF-G
and suggests further that this association is a result of gene duplication/fusion events. In support of this mechanism, the
three-dimensional structures of IF-3, EF-Tu, and EF-G display a predictable domain structure and overall conformational similarity.
The model that we propose consists of three consecutives duplication/fusion events which would have taken place before the
divergence of the three superkingdoms: eubacteria, archaea, and eukaryotes. The root of this protein superfamily tree would
be an ancestor of the modern IF-1 gene sequence. The repeated fundamental motif of this protein superfamily is a small RNA
binding domain composed of two α-helices packed along side of an antiparallel β-sheet.
Received: 17 October 1996 / Accepted: 10 June 1997 相似文献
10.
11.
The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering
based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of
the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were
exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology
to the cAMP-binding domains, and subsequently to the region delimited by β-strands 6 and 7 of the crystal structures of bovine
RIα and rat RIIβ (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally
the members of the PKA-R family. A single signature sequence, F–G–E–[LIV]–A–L–[LIMV]–x(3)–[PV]–R–[ANQV]–A, corresponding to
the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members
of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type
were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning
the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved
and are mostly located on the loop that connects α-helix B′ and β strand 7.
Received: 2 November 2000/Accepted: 14 June 2001 相似文献
12.
Gene structure of a chlorophyll a/c-binding protein from a brown alga: Presence of an intron and phylogenetic implications 总被引:5,自引:0,他引:5
Lise Caron Dominique Douady Michelle Quinet-Szely Susan de Goër Claire Berkaloff 《Journal of molecular evolution》1996,43(3):270-280
A Laminaria saccharina genomic library in the phage EMBL 4 was used to isolate and sequence a full-length gene encoding a fucoxanthin-chlorophyll
a/c-binding protein. Contrary to diatom homologues, the coding sequence is interrupted by an intron of about 900 bp which
is located in the middle of the transit peptide. The deduced amino acid sequence of the mature protein is very similar to
those of related proteins from Macrocystis pyrifera (Laminariales) and, to a lesser extent, to those from diatoms and Chrysophyceae. Seven of the eight putative chlorophyll-binding
amino acids determined in green plants are also present. Alignments of different sequences related to the light-harvesting
proteins (LHC) demonstrate a structural similarity among the three transmembrane helices and suggest a unique ancestral helix
preceded by two β-turns. The β-turns are conserved in front of the second helices of the chlorophyll a/c proteins more so
than in chlorophyll a/b proteins. Phylogenetic trees generated from sequence data indicate that fucoxanthin-chlorophyll-binding
proteins diverged prior to the separation of photosystem I and photosystem II LHC genes of green plants. Among the fucoxanthin-containing
algae, LHC I or II families could not be distinguished at this time.
Received: 14 February 1996 / Accepted: 4 April 1996 相似文献
13.
《Plant Physiology and Biochemistry》2000,38(9):685-698
The present project aimed to isolate testa-, pericarp- and epicarp-specific gene promoters for the developing caryopsis of barley (Hordeum vulgare L.). These might be applied in transgenic plants to express antifungal agents or modify metabolic pathways. A testa-specific 379-nucleotide fragment was cloned by differential amplification and used to screen a bacterial artificial chromosome (BAC) library of 6.3 haploid genome equivalents. Fifty-three clones containing genes encoding for proteins of the germin family were found. Characterization of the clones identified a minimum of six seed coat- and eight leaf-specific germin genes. Four seed coat- and one leaf-specific genes were sequenced. The deduced primary structure of the proteins revealed a remarkable conservation of the manganese(II) binding His and Glu residues and β-barrel secondary structure of oxalate oxidase – also in barley, wheat, rice and Arabidopsis germins, for which an enzymatic activity has not yet been identified. The oxalate oxidase and germins of barley and other species are synthesized with a conserved pre-sequence of 23 or 24 amino acids for targeting into the cell wall. β-Glucuronidase expression with the barley germin F gene promoter occurs specifically in the testa and epicarp of the developing barley caryopsis, while expression with the B gene promoter is restricted to the testa. Oxalate oxidase activity is prominent in the epicarp and the root tips of the developing embryo. A family tree based on primary structure homologies of germins distinguishes three groups: oxalate oxidases, leaf-specific germins and seed coat-specific germins. 相似文献
14.
Four subfamilies of c-type lysozyme and one subfamily of α-lactalbumin are defined from 78 sequences, and their folding nucleus is identified with
a method based on conserved residues and native structural contacts between pairs of conserved residues. One large cluster
of 19 conserved residues is found which is mostly nonpolar, buried, and nonfunctional. It can be subdivided into three subclusters:
(1) conserved residues in four helices; (2) conserved residues that stabilize the connector between the α and the β domains;
and (3) a β-turn, sitting in the middle of a bowl of α-helix residues. It is proposed that this folding nucleus initiates
four helices, A, B, C, and D, three β sheets, and the connector, which corresponds closely to the nucleation of the so-called
fast folding track pathway. As the secondary structures propagate, nonconserved residues and functionally conserved residues
would form additional contacts. The conserved residues are selected with a phylogenetic scheme in which single members of
subfamilies are selected. Subfamilies are then equally weighted to obtain the consensus conservation.
Received: 11 June 2001 / Accepted: 28 August 2001 相似文献
15.
David L. Thurlow Gina M. Pulido Kristen J. Millar 《Journal of molecular evolution》1997,44(6):686-689
The protein sequence of ATP/CTP:tRNA nucleotidyltransferase (cca) from Sulfolobus shibatae was used to search open reading frames in the genome of Methanococcus jannaschii. Translations of two unidentified open reading frames showed significant sequence similarity to portions of the Sulfolobus cca protein. When the two open reading frames were joined together, the expanded open reading frame was similar in sequence to
the entire Sulfolobus cca protein and displayed features of the active site signature sequence proposed for members of class I enzymes within the superfamily
of nucleotidyltransferases (Yue et al., 1996, RNA 2, 895–908). A possible UUG start codon was identified based on significant sequence similarity of the resulting amino-terminal
region to that of Sulfolobus, and on a six-base complementarity between an adjacent upstream sequence and Methanococcus 16S rRNA.
Received: 10 February 1997 相似文献
16.
Wytze T. Stam Jaap J. Beintema Rossana D’Avino Maurizio Tamburrini Guido di Prisco 《Journal of molecular evolution》1997,45(4):437-445
Amino acid sequences of α- and β-chains of human hemoglobin and of hemoglobins of coelacanth and 24 teleost fish species,
including 11 antarctic and two temperate Notothenioidei, were analyzed using maximum parsimony. Trees were derived for the
α- and β-chains separately and for tandemly arranged sequences, using the human and coelacanth sequences as outgroups in all
analyses. The topologies of the trees of the α-and β-chains are highly congruent and indicate a specific pattern of gene duplications
and gene expression of teleost hemoglobins which has not yet been investigated into more detail. The Notothenioid fish generally
contain a single major hemoglobin and often a second minor component. The α- and β-chains of the major components form a monophyletic
group in all investigated trees, with the nonantarctic Pseudaphritis as their sister taxon. The minor chains also are a monophyletic group and form an unresolved cluster with the major chains
and the hemoglobins of tuna and red gurnard. The Notothenioid families Nototheniidae and Bathydraconidae appear to be paraphyletic.
Received: 26 March 1997 / Accepted: 7 May 1997 相似文献
17.
Daniel Haydon Susan Lea Liz Fry Nick Knowles Alan R. Samuel David Stuart Mark E. J. Woolhouse 《Journal of molecular evolution》1998,46(4):465-475
The VP1 capsid protein of foot and mouth disease virus (FMDV) is highly polymorphic and contains several of the major immunogenic
sites important to effective antibody neutralization and subsequent viral clearance by the immune system. Whether this high
level of polymorphism is of adaptive value to the virus remains unknown. In this study we examined sequence data from a set
of 55 isolates in order to establish the nature of selective pressures acting on this gene. Using the known molecular structure
of VP1, the rates and ratios of different types of nonsynonymous and synonymous changes were compared between different parts
of the protein. All parts of the protein are subject to purifying selection, but this is greatest amongst those amino acid
residues within β-strands and is significantly reduced at residues exposed on the capsid surface, which include those residues
demonstrated by previous mutational analyses to permit the virus to escape from monoclonal antibody binding. The ratios of
nonsynonymous substitution resulting in various forms of physicochemically radical and conserved amino acid change were shown
to be largely equal throughout these different parts of the protein. There was a consistently higher level of nonsynonymous
and charge radical sites in those regions of the gene coding for residues exposed on the outer surface of the capsid and a
marked difference in the use of amino acids between surface and nonsurface regions of the protein. However, the analysis is
consistent with the hypothesis that the observed sequence variation arises where it is least likely to be disruptive to the
higher-order structure of the protein and is not necessarily due to positive Darwinian selection.
Received: 8 March 1997 / Accepted: 12 August 1997 相似文献
18.
19.
Alessandra Bonci Alessandra Chiesurin Patrizia Muscas Gian Maria Rossolini 《Journal of molecular evolution》1997,44(3):299-309
The structure of a Salmonella enterica serovar typhi gene located within the fim gene cluster and encoding a putative periplasmic chaperone-like protein involved in the assembly of type 1 pili was determined.
This gene, named fimC, has the ability to encode a 26-kDa polypeptide which is similar, at the sequence level, to the PapD periplasmic chaperonin
mediating the assembly of P pili of Escherichia coli, as well as to other periplasmic chaperone-like proteins involved in the biogenesis of pili or capsule-like structures of
various Gram-negative bacteria. A comprehensive search through the literature and sequence databases identified 31 (putative)
bacterial proteins that can be included in this protein family on the basis of sequence similarity. Results of a multiple
sequence comparison analysis showed that several residues, including most of those known to be critical in maintaining the
three-dimensional structure of PapD, are either conserved or conservatively substituted in all these proteins, suggesting
an overall similar folding for all of them. It was also evident that members of this family are clustered into different subfamilies
according to structural and phyletic data.
Received: 15 February 1996 / Accepted: 3 October 1996 相似文献
20.
Evolution of Chitin-Binding Proteins in Invertebrates 总被引:11,自引:0,他引:11
Analysis of a group of invertebrate proteins, including chitinases and peritrophic matrix proteins, reveals the presence
of chitin-binding domains that share significant amino acid sequence similarity. The data suggest that these domains evolved
from a common ancestor which may be a protein containing a single chitin-binding domain. The duplication and transposition
of this chitin-binding domain may have contributed to the functional diversification of chitin-binding proteins. Sequence
comparisons indicated that invertebrate and plant chitin binding domains do not share significant amino acid sequence similarity,
suggesting that they are not coancestral. However, both the invertebrate and the plant chitin-binding domains are cysteine-rich
and have several highly conserved aromatic residues. In plants, cysteines have been elucidated in maintaining protein folding
and aromatic amino acids in interacting with saccharides [Wright HT, Sanddrasegaram G, Wright CS (1991) J Mol Evol 33:283–294].
It is likely that these residues perform similar functions in invertebrates. We propose that the invertebrate and the plant
chitin-binding domains share similar mechanisms for folding and saccharide binding and that they evolved by convergent evolution.
Furthermore, we propose that the disulfide bonds and aromatic residues are hallmarks for saccharide-binding proteins.
Received: 2 March 1998 / Accepted: 17 July 1998 相似文献