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1.
L-Malate (MalDH) and L-lactate (LDH) dehydrogenases belong to the same family of NAD-dependent enzymes. To gain insight into molecular relationships within this family, we studied two hyperthermophilic (LDH-like) L-MalDH (proteins with LDH-like structure and MalDH enzymatic activity) from the archaea Archaeoglobus fulgidus (Af) and Methanococcus jannaschii (Mj). The structural parameters of these enzymes determined by neutron scattering and analytical centrifugation showed that the Af (LDH-like) L-MalDH is a dimer whereas the Mj (LDH-like) L-MalDH is a tetramer. The effects of high temperature, cofactor binding, and high phosphate concentration were studied. They did not modify the oligomeric state of either enzyme. The enzymatic activity of the dimeric Af (LDH-like) L-MalDH is controlled by a pH-dependent transition at pH 7 without dissociation of the subunits. The data were analyzed in the light of the crystallographic structure of the LDH-like L-MalDH from Haloarcula marismortui. This showed that a specific loop at the dimer-dimer contact regions in these enzymes controls the tetramer formation. 相似文献
2.
【目的】研究芽孢杆菌(Bacillus sp.) P38中乳酸脱氢酶对其产高光学纯L-乳酸(光学纯度>99%)的影响。【方法】全基因组测序显示在该菌中存在3个乳酸代谢关键酶,分别为L-乳酸脱氢酶(L-LDH)、D-乳酸脱氢酶(D-LDH)和苹果酸或L-乳酸脱氢酶(M/L-LDH)。通过将这3个酶进行异源表达、纯化与酶学特性分析,结合Native-PAGE、实时荧光定量PCR等方法,初步确定该菌高产光学纯L-乳酸的机理。【结果】Bacillus sp. P38中L-LDH对丙酮酸的催化活性(Kcat/Km值)最高,分别是D-LDH的2.9倍和M/L-LDH的4.3倍。其中M/L-LDH主要起L-LDH的功能。Native-PAGE实验中未检测到D-LDH活性。Bacillus sp. P38所有发酵阶段ldhL的转录水平均高于ldhD和ldhM/L。【结论】L-LDH是Bacillus sp. P38产高光学纯L-乳酸的主要关键酶。 相似文献
3.
Irimia A Vellieux FM Madern D Zaccaï G Karshikoff A Tibbelin G Ladenstein R Lien T Birkeland NK 《Journal of molecular biology》2004,335(1):343-356
The crystal structure of malate dehydrogenase from the hyperthermophilic archaeon Archeoglobus fulgidus, in complex with its cofactor NAD, was solved at 2.9A resolution. The crystal structure shows a compact homodimer with one coenzyme bound per subunit. The substrate binding site is occupied by a sulphate ion. In order to gain insight into adaptation mechanisms, which allow the protein to be stable and active at high temperatures, the 3D structure was compared to those of several thermostable and hyperthermostable homologues, and to halophilic malate dehydrogenase. The hyperthermostable A. fulgidus MalDH protein displays a reduction of the solvent-exposed surface, an optimised compact hydrophobic core, a high number of hydrogen bonds, and includes a large number of ion pairs at the protein surface. These features occur concomitantly with a reduced number of residues in the protein subunit, due to several deletions in loop regions. The loops are further stiffened by ion pair links with secondary structure elements. A. fulgidus malate dehydrogenase is the only dimeric protein known to date that belongs to the [LDH-like] MalDH family. All the other known members of this family are homo-tetramers. The crystal structures revealed that the association of the dimers to form tetramers is prevented by several deletions, taking place at the level of two loops that are known to be essential for the tetramerisation process within the LDH and [LDH-like] MalDH enzymes. 相似文献
4.
Tim Smilda Anne H. Kamminga Peter Reinders Wia Baron Johan E.T. van Hylckama Vlieg Jaap J. Beintema 《Journal of molecular evolution》2001,52(5):457-466
Enzymic and structural studies on Drosophila alcohol dehydrogenases and other short-chain dehydrogenases/reductases (SDRs) are presented. Like alcohol dehydrogenases
from other Drosophila species, the enzyme from D. simulans is more active on secondary than on primary alcohols, although ethanol is its only known physiological substrate. Several
secondary alcohols were used to determine the kinetic parameters kcat and Km. The results of these experiments indicate that the substrate-binding region of the enzyme allows optimal binding of a short
ethyl side-chain in a small binding pocket, and of a propyl or butyl side-chain in large binding pocket, with stereospecificity
for R(−) alcohols. At a high concentration of R(−) alcohols substrate activation occurs. The kcat and Km values determined under these conditions are about two-fold, and two orders of magnitude, respectively, higher than those
at low substrate concentrations.
Sequence alignment of several SDRs of known, and unknown three-dimensional structures, indicate the presence of several conserved
residues in addition to those involved in the catalyzed reactions. Structural roles of these conserved residues could be derived
from observations made on superpositioned structures of several SDRs with known structures. Several residues are conserved
in tetrameric SDRs, but not in dimeric ones. Two halohydrin-halide-lyases show significant homology with SDRs in the catalytic
domains of these enzymes, but they do not have the structural features required for binding NAD+. Probably these lyases descend from an SDR, which has lost the capability to bind NAD+, but the enzyme reaction mechanisms may still be similar.
Received: 23 May 2000 / Accepted: 4 January 2001 相似文献
5.
Primary Structure and Phylogenetic Relationships of a Malate Dehydrogenase Gene from Giardia lamblia
The lactate and malate dehydrogenases comprise a complex protein superfamily with multiple enzyme homologues found in eubacteria,
archaebacteria, and eukaryotes. In this study we describe the sequence and phylogenetic relationships of a malate dehydrogenase
(MDH) gene from the amitochondriate diplomonad protist, Giardia lamblia. Parsimony, distance, and maximum-likelihood analyses of the MDH protein family solidly position G. lamblia MDH within a eukaryote cytosolic MDH clade, to the exclusion of chloroplast, mitochondrial, and peroxisomal homologues. Furthermore,
G. lamblia MDH is specifically related to a homologue from Trichomonas vaginalis. This MDH topology, together with published phylogenetic analyses of β-tubulin, chaperonin 60, valyl-tRNA synthetase, and
EF-1α, suggests a sister-group relationship between diplomonads and parabasalids. Since these amitochondriate lineages contain
genes encoding proteins which are characteristic of mitochondria and α-proteobacteria, their shared ancestry suggests that
mitochondrial properties were lost in the common ancestor of both groups.
Received: 14 September 1998 / Accepted: 29 December 1998 相似文献
6.
7.
L-Malate (MalDH) and L-lactate (LDH) dehydrogenases belong to the same family of NAD-dependent enzymes. LDHs are tetramers, whereas MalDHs can be either dimeric or tetrameric. To gain insight into molecular relationships between LDHs and MalDHs, we studied folding intermediates of a mutant of the LDH-like MalDH (a protein with LDH-like structure and MalDH enzymatic activity) from the halophilic archaeon Haloarcula marismortui (Hm MalDH). Crystallographic analysis of Hm MalDH had shown a tetramer made up of two dimers interacting mainly via complex salt bridge clusters. In the R207S/R292S Hm MalDH mutant, these salt bridges are disrupted. Its structural parameters, determined by neutron scattering and analytical centrifugation under different conditions, showed the protein to be a tetramer in 4 M NaCl. At lower salt concentrations, stable oligomeric intermediates could be trapped at a given pH, temperature, or NaCl solvent concentration. The spectroscopic properties and enzymatic behavior of monomeric, dimeric, and tetrameric species were thus characterized. The properties of the dimeric intermediate were compared to those of dimeric intermediates of LDH and dimeric MalDHs. A detailed analysis of the putative dimer-dimer contact regions in these enzymes provided an explanation of why some can form tetramers and others cannot. The study presented here makes Hm MalDH the best characterized example so far of an LDH-like MalDH. 相似文献
8.
The immunoglobulin superfamily (IgSF) is a heterogenic group of proteins built on a common fold, called the Ig fold, which
is a sandwich of two β sheets. Although members of the IgSF share a similar Ig fold, they differ in their tissue distribution,
amino acid composition, and biological role.
In this paper we report an up-to-date compilation of the IgSF where all known members of the IgSF are classified on the basis
of their common functional role (immune system, antibiotic proteins, enzymes, cytokine receptors, etc.) and their distribution
in tissue (neural system, extracellular matrix, tumor marker, muscular proteins, etc.), or in species (vertebrates, invertebrates,
bacteria, viruses, fungi, and plants). The members of the family can contain one or many Ig domains, comprising two basic
types: the constant domain (C), with seven strands, and the variable domain (V), with eight, nine, or ten strands. The different
overviews of the IgSF led to the definition of new domain subtypes, mainly concerning the C type, based on the distribution
of strands within the two sheets.
The wide occurrence of the Ig fold and the much less conserved sequences could have developed from a common ancestral gene
and/or from a convergent evolutionary process. Cell adhesion and pattern recognition seem to be the common feature running
through the entire family.
Received: 4 June 1997 / Accepted: 15 September 1997 相似文献
9.
One of the most debated issues concerning the origin of life, is how enzymes which are essential for existence of any living
organism, evolved. It is clear that, regardless of the exact mechanism, the process should have been specific and reproducible,
involving interactions between different molecules. We propose that substrate templating played a crucial role in maintaining
reproducible and specific formation of prebiotic catalysts. This work demonstrates experimentally, for the first time, substrate-directed
formation of an oligopeptide that possesses a specific catalytic activity toward the substrate on which it was formed. In
our experiments we used the substrate o-nitrophenol-β-d-galactopyranoside (ONPG) as a molecular template for the synthesis of a specific catalyst that is capable of cleaving the
same substrate. This was achieved by incubation of the substrate with free amino acids and a condensing agent (dicyandiamide)
at elevated temperatures. A linear increase with time of the reaction rate (d[product]/d2t), pointed to an acceleration regime, where the substrate generates the formation of the catalyst. The purified catalyst,
produced by a substrate-directed mechanism, was analyzed, and identified as Cys2-Fe+2. The mechanism of substrate-directed formation of prebiotic catalysts provides a solution to both the specificity and the
reproducibility requirements from any prebiotic system which should evolve into the biological world.
Received: 26 January 1996 / Accepted: 22 April 1997 相似文献
10.
Intracellular Domains of Mouse Connexin26 and -30 Affect Diffusional and Electrical Properties of Gap Junction Channels 总被引:5,自引:0,他引:5
D. Manthey K. Banach T. Desplantez C.G. Lee C.A. Kozak O. Traub R. Weingart K. Willecke 《The Journal of membrane biology》2001,181(2):137-148
To evaluate the influence of intracellular domains of connexin (Cx) on channel transfer properties, we analyzed mouse connexin
(Cx) Cx26 and Cx30, which show the most similar amino acid sequence identities within the family of gap junction proteins.
These connexin genes are tightly linked on mouse chromosome 14. Functional studies were performed on transfected HeLa cells
stably expressing both mouse connexins. When we examined homotypic intercellular transfer of microinjected neurobiotin and
Lucifer yellow, we found that gap junctions in Cx30-transfected cells, in contrast to Cx26 cells, were impermeable to Lucifer
yellow. Furthermore, we observed heterotypic transfer of neurobiotin between Cx30-transfectants and HeLa cells expressing
mouse Cx30.3, Cx40, Cx43 or Cx45, but not between Cx26 transfectants and HeLa cells of the latter group. The main differences
in amino acid sequence between Cx26 and Cx30 are located in the presumptive cytoplasmic loop and C-terminal region of these
integral membrane proteins. By exchanging one or both of these domains, using PCR-based mutagenesis, we constructed Cx26/30
chimeric cDNAs, which were also expressed in HeLa cells after transfection. Homotypic intercellular transfer of injected Lucifer
yellow was observed exclusively with those chimeric constructs that coded for both cytoplasmic domains of Cx26 in the Cx30
backbone polypeptide chain. In contrast, cells transfected with a construct that coded for the Cx26 backbone with the Cx30
cytoplasmic loop and C-terminal region did not show transfer of Lucifer yellow. Thus, Lucifer yellow transfer can be conferred
onto chimeric Cx30 channels by exchanging the cytoplasmic loop and the C-terminal region of these connexins. In turn, the
cytoplasmic loop and C-terminal domain of Cx30 prevent Lucifer yellow transfer when swapped with the corresponding domains
of Cx26. In chimeric Cx30/Cx26 channels where the cytoplasmic loop and C-terminal domains had been exchanged, the unitary
channel conductance was intermediate between those of the parental channels. Moreover, the voltage sensitivity was slightly
reduced. This suggests that these cytoplasmic domains interfere directly or indirectly with the diffusivity, the conductance
and voltage gating of the channels.
Received: 26 July 2000/Revised: 15 February 2001 相似文献
11.
C. R. Goward D. J. Nicholls 《Protein science : a publication of the Protein Society》1994,3(10):1883-1888
Malate dehydrogenases are widely distributed and alignment of the amino acid sequences show that the enzyme has diverged into 2 main phylogenetic groups. Multiple amino acid sequence alignments of malate dehydrogenases also show that there is a low degree of primary structural similarity, apart from in several positions crucial for nucleotide binding, catalysis, and the subunit interface. The 3-dimensional structures of several malate dehydrogenases are similar, despite their low amino acid sequence identity. The coenzyme specificity of malate dehydrogenase may be modulated by substitution of a single residue, as can the substrate specificity. The mechanism of catalysis of malate dehydrogenase is similar to that of lactate dehydrogenase, an enzyme with which it shares a similar 3-dimensional structure. Substitution of a single amino acid residue of a lactate dehydrogenase changes the enzyme specificity to that of a malate dehydrogenase, but a similar substitution in a malate dehydrogenase resulted in relaxation of the high degree of specificity for oxaloacetate. Knowledge of the 3-dimensional structures of malate and lactate dehydrogenases allows the redesign of enzymes by rational rather than random mutation and may have important commercial implications. 相似文献
12.
One of the most remarkable biochemical differences between the members of two domains Archaea and Bacteria is the stereochemistry
of the glycerophosphate backbone of phospholipids, which are exclusively opposite. The enzyme responsible to the formation
of Archaea-specific glycerophosphate was found to be NAD(P)-linked sn-glycerol-1-phosphate (G-1-P) dehydrogenase and it was first purified from Methanobacterium thermoautotrophicum cells and its gene was cloned. This structure gene named egsA (enantiomeric glycerophosphate synthase) consisted of 1,041 bp and coded the enzyme with 347 amino acid residues. The amino
acid sequence deduced from the base sequence of the cloned gene (egsA) did not share any sequence similarity except for NAD-binding region with that of NAD(P)-linked sn-glycerol-3-phosphate (G-3-P) dehydrogenase of Escherichia coli which catalyzes the formation of G-3-P backbone of bacterial phospholipids, while the deduced protein sequence of the enzyme
revealed some similarity with bacterial glycerol dehydrogenases. Because G-1-P dehydrogenase and G-3-P dehydrogenase would
originate from different ancestor enzymes and it would be almost impossible to interchange stereospecificity of the enzymes,
it seems likely that the stereostructure of membrane phospholipids of a cell must be maintained from the time of birth of
the first cell. We propose here the hypothesis that Archaea and Bacteria were differentiated by the occurrence of cells enclosed
by membranes of phospholipids with G-1-P and G-3-P as a backbone, respectively.
Received: 24 March 1997 / Accepted: 21 May 1997 相似文献
13.
Albert Jeltsch 《Journal of molecular evolution》1999,49(1):161-164
Circular permutations of genes during molecular evolution often are regarded as elusive, although a simple model can explain
these rearrangements. The model assumes that first a gene duplication of the precursor gene occurs in such a way that both
genes become fused in frame, leading to a tandem protein. After generation of a new start codon within the 5′ part of the
tandem gene and a stop at an equivalent position in the 3′ part of the gene, a protein is encoded that represents a perfect
circular permutation of the precursor gene product. The model is illustrated here by the molecular evolution of adenine-N6 DNA methyltransferases. β- and γ-type enzymes of this family can be interconverted by a single circular permutation event.
Interestingly, tandem proteins, proposed as evolutionary intermediates during circular permutation, can be directly observed
in the case of adenine methyltransferases, because some enzymes belonging to type IIS, like the FokI methyltransferase, are built up by two fused enzymes, both of which are active independently of each other. The mechanism
for circular permutation illustrated here is very easy and applicable to every protein. Thus, circular permutation can be
regarded as a normal process in molecular evolution and a changed order of conserved amino acid motifs should not be interpreted
to argue against divergent evolution.
Received: 17 November 1998 / Accepted: 19 February 1999 相似文献
14.
We analyzed the phylogenetic relationship between the species of Lordiphosa and other Drosophilidae using alcohol dehydrogenase (Adh) gene sequences. The phylogenetic trees consistently show that the four species Drosophila kurokawai, D. collinella, D. stackelbergi, and D. clarofinis, which include three species groups of Lordiphosa, form a monophyletic clade. This clade is placed as a sister group to the willistoni and saltans groups of Sophophora. On the other hand, three species of Lordiphosa, D. tenuicauda, D. pseudotenuicauda, and D. acutissima, all of which belong to the tenuicauda group, are not shown to be related to the major Lordiphosa lineage. In the phylogenetic trees, these species are included into the clade comprised of Drosophila and Hirtodrosophila, although it remains uncertain whether the tenuicauda group is a monophyletic group or not. These results indicate that Lordiphosa is polyphyletic and that most of the members of the subgenus have a close relationship to the neotropical groups of Sophophora. The above conclusion is compatible with the hypothesis of Okada (Mushi [1963] 37:79–100) and Lastovka and Máca (Acta Ent Bohemoslov [1978] 75:404–420) that Lordiphosa is most closely related to Sophophora; in contrast, our results contradict the hypothesis of Grimaldi (Bull Am Mus Nat Hist [1990] 197:1–139) that Lordiphosa is a sister group to the genus Scaptomyza.
Received: 12 May 1999 / Accepted: 14 April 2000 相似文献
15.
Jen-Jen Lin Tzung-Horng Yang Benjamin D. Wahlstrand Peter A. Fields George N. Somero 《Journal of molecular evolution》2002,54(1):107-117
Unlike birds and mammals, teleost fish express two paralogous isoforms (paralogues) of cytosolic malate dehydrogenase (cMDH;
EC 1.1.1.37; NAD+: malate oxidoreductase) whose evolutionary relationships to the single cMDH of tetrapods are unknown. We sequenced complementary
DNAs for both cMDHs and the mitochondrial isoform (mMDH) of the fish Sphyraena idiastes (south temperate barracuda) and compared the sequences, kinetic properties, and thermal stabilities of the three isoforms
with those of mammalian orthologues. Both fish cMDHs comprise 333 residues and have subunit masses of approximately 36 kDa.
One cytosolic isoform, cMDH-S, was significantly more heat-stable than either the other cMDH (cMDH-L) or mMDH. In contradiction
to the generally accepted model of vertebrate cMDH evolution, our phylogenetic analysis indicates that the duplication of
the fish cytosolic paralogues occurred after the divergence of the lineages leading to teleosts and tetrapods. cMDH-L and
cMDH-S differed in optimal concentrations of substrates and cofactors and apparent Michaelis–Menten constants, suggesting
that the two paralogues may play distinct physiological roles. Differences in intrinsic thermal stability among MDH paralogues
may reflect different degrees of stabilization in vivo by extrinsic stabilizers, notably protein concentration in the case
of mMDH. Thermal stabilities of porcine mMDH and cMDH-L, but not cMDH-S, were significantly increased when denaturation was
measured at a high protein (bovine serum albumin; BSA) concentration, but the BSA-induced stabilization reduced the catalytic
activity.
Received: 5 April 2001 / Accepted: 28 June 2001 相似文献
16.
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
17.
Heat Shock Protein 70 Family: Multiple Sequence Comparisons, Function, and Evolution 总被引:14,自引:0,他引:14
The heat shock protein 70 kDa sequences (HSP70) are of great importance as molecular chaperones in protein folding and transport.
They are abundant under conditions of cellular stress. They are highly conserved in all domains of life: Archaea, eubacteria,
eukaryotes, and organelles (mitochondria, chloroplasts). A multiple alignment of a large collection of these sequences was
obtained employing our symmetric-iterative ITERALIGN program (Brocchieri and Karlin 1998). Assessments of conservation are
interpreted in evolutionary terms and with respect to functional implications. Many archaeal sequences (methanogens and halophiles)
tend to align best with the Gram-positive sequences. These two groups also miss a signature segment [about 25 amino acids
(aa) long] present in all other HSP70 species (Gupta and Golding 1993). We observed a second signature sequence of about 4
aa absent from all eukaryotic homologues, significantly aligned in all prokaryotic sequences. Consensus sequences were developed
for eight groups [Archaea, Gram-positive, proteobacterial Gram-negative, singular bacteria, mitochondria, plastids, eukaryotic
endoplasmic reticulum (ER) isoforms, eukaryotic cytoplasmic isoforms]. All group consensus comparisons tend to summarize better
the alignments than do the individual sequence comparisons. The global individual consensus ``matches' 87% with the consensus
of consensuses sequence. A functional analysis of the global consensus identifies a (new) highly significant mixed charge
cluster proximal to the carboxyl terminus of the sequence highlighting the hypercharge run EEDKKRRER (one-letter aa code used).
The individual Archaea and Gram-positive sequences contain a corresponding significant mixed charge cluster in the location
of the charge cluster of the consensus sequence. In contrast, the four Gram-negative proteobacterial sequences of the alignment
do not have a charge cluster (even at the 5% significance level). All eukaryotic HSP70 sequences have the analogous charge
cluster. Strikingly, several of the eukaryotic isoforms show multiple mixed charged clusters. These clusters were interpreted
with supporting data related to HSP70 activity in facilitating chaperone, transport, and secretion function. We observed that
the consensus contains only a single tryptophan residue and a single conserved cysteine. This is interpreted with respect
to the target rule for disaggregating misfolded proteins. The mitochondrial HSP70 connections to bacterial HSP70 are analyzed,
suggesting a polyphyletic split of Trypanosoma and Leishmania protist mitochondrial (Mt) homologues separated from Mt-animal/fungal/plant homologues. Moreover, the HSP70 sequences from
the amitochondrial Entamoeba histolytica and Trichomonas vaginalis species were analyzed. The E. histolytica HSP70 is most similar to the higher eukaryotic cytoplasmic sequences, with significantly weaker alignments to ER sequences
and much diminished matching to all eubacterial, mitochondrial, and chloroplast sequences. This appears to be at variance
with the hypothesis that E. histolytica rather recently lost its mitochondrial organelle. T. vaginalis contains two HSP70 sequences, one Mt-like and the second similar to eukaryotic cytoplasmic sequences suggesting two diverse
origins.
Received: 29 January 1998 / Accepted: 14 May 1998 相似文献
18.
Specific antisera against glycogen phosphorylase, phosphofructokinase, aldolase, glyceraldehyde-phosphate dehydrogenase, enolase, lactate dehydrogenase, cytosolic and mitochondrial malate dehydrogenase from rabbit muscle were obtained from sheep. The gamma-globulins were used for indirect immunofluorescent localization of the respective enzymes in rabbit skeletal muscle and heart. In stretched skeletal muscle a cross-striation like distribution was observed for all enzymes studied. In the case of mitochondrial malate dehydrogenase this pattern is due to the staining of I-band mitochondria. In cross-sections, an intense staining of the sarcolemma and of subsarcolemmal mitochondria was observed. Comparative analyses with polarized light revealed that the cytosolic enzymes under study are distributed in the relaxed muscle fibre predominantly within the isotropic zones. The same distribution holds also for heart. In contracting muscle a decrease in cross-striated fluorescence and a faint staining of the interfibrillar spaces suggests a location also within the interfibrillar space. 相似文献
19.
Bujnicki JM 《Journal of molecular evolution》2000,50(1):39-44
To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments
have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the
first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates
of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic
analyses. It is shown that λ-exonuclease initially diverged from the common ancestor and then two ``endonucleolytic' families
branched out, separating ``blunt end cutters' from ``5′ four-base overhang cutters.' These data may contribute to a better
understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among
extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a
platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational
choice of homology modeling templates, and targets for protein engineering.
Received: 14 June 1999 / Accepted: 11 August 1999 相似文献
20.
Francine Hamel Rodolphe Boivin Colette Tremblay Guy Bellemare 《Journal of molecular evolution》1997,44(6):614-624
The analysis of nuclear-encoded chitinase sequences from various angiosperms has allowed the categorization of the chitinases
into discrete classes. Nucleotide sequences of their catalytic domains were compared in this study to investigate the evolutionary
relationships between chitinase classes. The functionally distinct class III chitinases appear to be more closely related
to fungal enzymes involved in morphogenesis than to other plant chitinases. The ordering of other plant chitinases into additional
classes mainly relied on the presence of auxiliary domains—namely, a chitin-binding domain and a carboxy-terminal extension—flanking
the main catalytic domain. The results of our phylogenetic analyses showed that classes I and IV form discrete and well-supported
monophyletic groups derived from a common ancestral sequence that predates the divergence of dicots and monocots. In contrast,
other sequences included in classes I* and II, lacking one or both types of auxiliary domains, were nested within class I
sequences, indicating that they have a polyphyletic origin. According to phylogenetic analyses and the calculation of evolutionary
rates, these chitinases probably arose from different class I lineages by relatively recent deletion events. The occurrence
of such evolutionary trends in cultivated plants and their potential involvement in host–pathogen interactions are discussed.
Received: 5 July 1996 / Accepted: 9 January 1997 相似文献