Searching for amino acid sequence motifs among enzymes: the Enzyme–Reaction Database

1993 ◽  
Vol 9 (1) ◽  
pp. 9-15 ◽  
Author(s):  
Mikita Suyama ◽  
Atsushi Ogiwara ◽  
Takaaki Nishioka ◽  
Jun'ichi Oda
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Enzyme Reaction ◽  
Sequence Motifs

scholarly journals Rhodococcus sp. Strain CR-53 LipR, the First Member of a New Bacterial Lipase Family (Family X) Displaying an Unusual Y-Type Oxyanion Hole, Similar to the Candida antarctica Lipase Clan

2012 ◽  
Vol 78 (6) ◽  
pp. 1724-1732 ◽  
Author(s):  
Arnau Bassegoda ◽  
F. I. Javier Pastor ◽  
Pilar Diaz
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Candida Antarctica ◽  
Burkholderia Cenocepacia ◽  
Sequence Motifs ◽  
Oxyanion Hole ◽  
Content Type ◽  
New Family ◽  
Consensus Amino Acid Sequence ◽  
Four Blocks

ABSTRACTBacterial lipases constitute the most important group of biocatalysts for synthetic organic chemistry. Accordingly, there is substantial interest in developing new valuable lipases. Considering the lack of information concerning the lipases of the genusRhodococcusand taking into account the interest raised by the enzymes produced by actinomycetes, a search for putative lipase-encoding genes fromRhodococcussp. strain CR-53 was performed. We isolated, cloned, purified, and characterized LipR, the first lipase described from the genusRhodococcus. LipR is a mesophilic enzyme showing preference for medium-chain-length acyl groups without showing interfacial activation. It displays good long-term stability and high tolerance for the presence of ions and chemical agents in the reaction mixture. Amino acid sequence analysis of LipR revealed that it displays four unique amino acid sequence motifs that clearly separate it from any other previously described family of bacterial lipases. Using bioinformatics tools, LipR could be related only to several uncharacterized putative lipases from different bacterial origins, all of which display the four blocks of consensus amino acid sequence motifs that contribute to define a new family of bacterial lipases, namely, family X. Therefore, LipR is the first characterized member of the new bacterial lipase family X. Further confirmation of this new family of lipases was performed after cloningBurkholderia cenocepaciaputative lipase, bearing the same conserved motifs and clustering in family X. Interestingly, all lipases grouping in the new bacterial lipase family X display a Y-type oxyanion hole, a motif conserved in theCandida antarcticalipase clan but never found among bacterial lipases. This observation contributes to confirm that LipR and its homologs belong to a new family of bacterial lipases.

scholarly journals Short translational ramp determines efficiency of protein synthesis

2019 ◽  
Author(s):  
Manasvi Verma ◽  
Junhong Choi ◽  
Kyle A. Cottrell ◽  
Zeno Lavagnino ◽  
Erica N. Thomas ◽  
...  
Keyword(s):  
Protein Synthesis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Single Molecule ◽  
Translation Initiation ◽  
Protein Translation ◽  
Translational Efficiency ◽  
Translation Efficiency ◽  
Sequence Motifs ◽  
Peptide Bond Formation

AbstractIt is generally assumed that translation efficiency is governed by translation initiation. However, the efficiency of protein synthesis is regulated by multiple factors including tRNA abundance, codon composition, mRNA motifs and amino-acid sequence1–4. These factors influence the rate of protein synthesis beyond the initiation phase of translation, typically by modulating the rate of peptide-bond formation and to a lesser extent that of translocation. The slowdown in translation during the early elongation phase, known as the 5’ translational ramp, likely contributes to the efficiency of protein synthesis 5–9. Multiple mechanisms, which could explain the molecular basis for this translational ramp, have been proposed that include tRNA abundance bias6,9, the rate of translation initiation10–15, mRNA and ribosome structure 11,12,14,16–18, or retention of initiation factors during early elongation events 19. Here, we show that the amount of synthesized protein (translation efficiency) depends on a short translational ramp that comprises the first 5 codons in mRNA. Using a library of more than 250,000 reporter sequences combined with in vitro and in vivo protein expression assays, we show that differences in the short ramp can lead to 3 to 4 orders of magnitude changes in protein abundance. The observed difference is not dependent on tRNA abundance, efficiency of translation initiation, or overall mRNA structure. Instead, we show that translation is regulated by amino-acid-sequence composition and local mRNA sequence. Single-molecule measurements of translation kinetics indicate substantial pausing of ribosome and abortion of protein synthesis on the 4th or 5th codon for distinct amino acid or nucleotide compositions. Introduction of preferred sequence motifs, only at the exact positions within the mRNA, improves protein synthesis for recombinant proteins, indicating an evolutionarily conserved mechanism for controlling translational efficiency.

scholarly journals A 19 kDa protein secreted by the endometrium of the mare is a novel member of the lipocalin family

1996 ◽  
Vol 320 (1) ◽  
pp. 137-143 ◽  
Author(s):  
Ben CROSSETT ◽  
W. R. ALLEN ◽  
Francesca STEWART
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Southern Blot ◽  
Blot Analysis ◽  
Southern Blot Analysis ◽  
Single Gene ◽  
Expression Patterns ◽  
Dimensional Structure ◽  
Predicted Amino Acid Sequence ◽  
Sequence Motifs

Large quantities of an unusual 19 kDa protein (p19) are secreted into the lumen of the uterus of the mare (Equus caballus) during the oestrous cycle and early pregnancy. p19 associates strongly with the acellular capsule that surrounds the young horse conceptus and is believed to be important in maintaining pregnancy. Here we report the complete cDNA sequence encoding p19, its expression patterns in horse tissues and a Southern blot analysis of the gene in horse DNA. The predicted amino acid sequence of the p19 cDNA demonstrated a signal peptide of 18 residues and a mature protein of 162 residues, giving a predicted molecular mass of 18.8 kDa for the secreted protein. Analysis of the predicted amino acid sequence showed that p19 belongs to the lipocalin family of proteins, which are classified on the basis of three conserved amino acid sequence motifs and an eight-stranded anti-parallel β-barrel conformation. Overall, p19 was most similar to the mouse major urinary protein (MUP) lipocalins (30–34% identity). Secondary structural predictions and structural modelling using the MUP 1 crystal structure coordinates gave convincing evidence that the three-dimensional structure of p19 closely resembles that of the lipocalins. However, p19 has several unusual substitutions in one of the three conserved lipocalin motifs and therefore seems to be a novel member of the family. Lipocalins perform many different functions but most bind small hydrophobic molecules and the majority act as transport proteins. The function of p19 might therefore be as a carrier of a maternal factor needed to sustain the developing embryo during pregnancy, or it could be incorporated into the embryonic capsule and perform some other function. Northern blot analysis demonstrated that expression of p19 is confined to the endometrial lining of the mare's uterus, and hybridization studies in situ showed that the mRNA for p19 is localized to the glandular and luminal epithelia of the endometrium. A Southern blot analysis of horse DNA indicated a single gene for p19 that seems to be at least 4.5 kb in size.

Amino‐acid sequence motifs for PKC‐mediated membrane trafficking of the inhibitory killer Ig‐like receptor

2008 ◽  
Vol 86 (4) ◽  
pp. 372-380 ◽  
Author(s):  
Yong‐Joon Chwae ◽  
Jae Myun Lee ◽  
Hyung‐Ran Kim ◽  
Eun Joo Kim ◽  
Seung Tae Lee ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Membrane Trafficking ◽  
Sequence Motifs

scholarly journals Defining Electron Bifurcation in the Electron-Transferring Flavoprotein Family

2017 ◽  
Vol 199 (21) ◽  
Author(s):  
Amaya M. Garcia Costas ◽  
Saroj Poudel ◽  
Anne-Frances Miller ◽  
Gerrit J. Schut ◽  
Rhesa N. Ledbetter ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Energy Conservation ◽  
Structural Modeling ◽  
Sequence Motifs ◽  
Quinone Oxidoreductase ◽  
Sequence Alignments ◽  
Electron Transfer Mechanism ◽  
Electron Transferring Flavoprotein

ABSTRACT Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low- and high-potential electrons. It is the third recognized form of energy conservation in biology and was recently described for select electron-transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via Etf-quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer, as well as a non-redox-active AMP. However, Etfs demonstrated to bifurcate electrons contain a second FAD in place of the AMP. To expand our understanding of the functional variety and metabolic significance of Etfs and to identify amino acid sequence motifs that potentially enable electron bifurcation, we compiled 1,314 Etf protein sequences from genome sequence databases and subjected them to informatic and structural analyses. Etfs were identified in diverse archaea and bacteria, and they clustered into five distinct well-supported groups, based on their amino acid sequences. Gene neighborhood analyses indicated that these Etf group designations largely correspond to putative differences in functionality. Etfs with the demonstrated ability to bifurcate were found to form one group, suggesting that distinct conserved amino acid sequence motifs enable this capability. Indeed, structural modeling and sequence alignments revealed that identifying residues occur in the NADH- and FAD-binding regions of bifurcating Etfs. Collectively, a new classification scheme for Etf proteins that delineates putative bifurcating versus nonbifurcating members is presented and suggests that Etf-mediated bifurcation is associated with surprisingly diverse enzymes. IMPORTANCE Electron bifurcation has recently been recognized as an electron transfer mechanism used by microorganisms to maximize energy conservation. Bifurcating enzymes couple thermodynamically unfavorable reactions with thermodynamically favorable reactions in an overall spontaneous process. Here we show that the electron-transferring flavoprotein (Etf) enzyme family exhibits far greater diversity than previously recognized, and we provide a phylogenetic analysis that clearly delineates bifurcating versus nonbifurcating members of this family. Structural modeling of proteins within these groups reveals key differences between the bifurcating and nonbifurcating Etfs.

The tail domains of keratins contain conserved amino acid sequence motifs

2009 ◽  
Vol 54 (3) ◽  
pp. 208-209 ◽  
Author(s):  
Leopold Eckhart ◽  
Karin Jaeger ◽  
Erwin Tschachler
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Motifs
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