scholarly journals Simulating evolution by gene duplication of protein features that require multiple amino acid residues

2009 ◽  
Vol 13 (10) ◽  
pp. 2651-2664 ◽  
Author(s):  
Michael J. Behe ◽  
David W. Snoke
Keyword(s):  
Amino Acid ◽  
Gene Duplication ◽  
Amino Acid Residues ◽  
Multiple Amino Acid

CDDO-imidazolide Targets Multiple Amino Acid Residues on the Nrf2 Adaptor, Keap1

2020 ◽  
Vol 63 (17) ◽  
pp. 9965-9976 ◽  
Author(s):  
Xiaoli Meng ◽  
James C. Waddington ◽  
Arun Tailor ◽  
Adam Lister ◽  
Jane Hamlett ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Residues ◽  
Multiple Amino Acid

scholarly journals Cloning and Sequence Analysis of a New Cellulase Gene Encoding CelK, a Major Cellulosome Component of Clostridium thermocellum: Evidence for Gene Duplication and Recombination

1999 ◽  
Vol 181 (17) ◽  
pp. 5288-5295 ◽  
Author(s):  
Irina Kataeva ◽  
Xin-Liang Li ◽  
Huizhong Chen ◽  
Sang-Ki Choi ◽  
Lars G. Ljungdahl
Keyword(s):  
Amino Acid ◽  
Gene Duplication ◽  
Signal Peptide ◽  
Clostridium Thermocellum ◽  
Catalytic Domain ◽  
Glycosyl Hydrolase ◽  
Size Difference ◽  
Amino Acid Residues ◽  
Cellulase Gene ◽  
Original Activity

ABSTRACT The cellulolytic and hemicellulolytic complex of Clostridium thermocellum, termed cellulosome, consists of up to 26 polypeptides, of which at least 17 have been sequenced. They include 12 cellulases, 3 xylanases, 1 lichenase, and CipA, a scaffolding polypeptide. We report here a new cellulase gene, celK, coding for CelK, a 98-kDa major component of the cellulosome. The gene has an open reading frame (ORF) of 2,685 nucleotides coding for a polypeptide of 895 amino acid residues with a calculated mass of 100,552 Da. A signal peptide of 27 amino acid residues is cut off during secretion, resulting in a mature enzyme of 97,572 Da. The nucleotide sequence is highly similar to that of cbhA(V. V. Zverlov et al., J. Bacteriol. 180:3091–3099, 1998), having an ORF of 3,690 bp coding for the 1,230-amino-acid-residue CbhA of the same bacterium. Homologous regions of the two genes are 86.5 and 84.3% identical without deletion or insertion on the nucleotide and amino acid levels, respectively. Both have domain structures consisting of a signal peptide, a family IV cellulose binding domain (CBD), a family 9 glycosyl hydrolase domain, and a dockerin domain. A striking distinction between the two polypeptides is that there is a 330-amino-acid insertion in CbhA between the catalytic domain and the dockerin domain containing a fibronectin type 3-like domain and family III CBD. This insertion, missing in CelK, is responsible for the size difference between CelK and CbhA. Upstream and downstream flanking sequences of the two genes show no homology. The data indicate thatcelK and cbhA in the genome of C. thermocellum have evolved through gene duplication and recombination of domain coding sequences. celK without a dockerin domain was expressed in Escherichia coli and purified. The enzyme had pH and temperature optima at 6.0 and 65°C, respectively. It hydrolyzedp-nitrophenyl-β-d-cellobioside with aKm and a V max of 1.67 μM and 15.1 U/mg, respectively. Cellobiose was a strong inhibitor of CelK activity, with a Ki of 0.29 mM. The enzyme was thermostable, after 200 h of incubation at 60°C, 97% of the original activity remained. Properties of the enzyme indicated that it is a cellobiohydrolase.

scholarly journals Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin

BIOPHYSICS ◽  
2010 ◽  
Vol 6 ◽  
pp. 67-78 ◽  
Author(s):  
Hiroshi C. Watanabe ◽  
Yoshiharu Mori ◽  
Takashi Tada ◽  
Shozo Yokoyama ◽  
Takahisa Yamato
Keyword(s):  
Amino Acid ◽  
Molecular Mechanism ◽  
Long Range ◽  
Amino Acid Residues ◽  
Color Tuning ◽  
Multiple Amino Acid

scholarly journals An Evolutionary Perspective of the Lipocalin Protein Family

2021 ◽  
Vol 12 ◽  
Author(s):  
Sergio Diez-Hermano ◽  
Maria D. Ganfornina ◽  
Arne Skerra ◽  
Gabriel Gutiérrez ◽  
Diego Sanchez
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Family ◽  
Gene Duplications ◽  
Amino Acid Residues ◽  
Sequence Alignments ◽  
New Members ◽  
Multiple Amino Acid ◽  
Sequence Similarities ◽  
Tandem Duplications

The protein family of Lipocalins is ubiquitously present throughout the tree of life, with the exception of the phylum Archaea. Phylogenetic relationships of chordate Lipocalins have been proposed in the past based on protein sequence similarities, but their highly divergent primary structures and a shortage of experimental annotations in genome projects have precluded a well-supported hypothesis for their evolution. In this work we propose a novel topology for the phylogenetic tree of chordate Lipocalins, inferred from multiple amino acid sequence alignments. Sixteen jawed vertebrates with fair coverage by genomic sequencing were compared. The selected species span an evolutionary range of ∼400 million years, allowing for a balanced representation of all major vertebrate clades. A consensus phylogenetic tree is proposed following a comparison of sequence-based maximum-likelihood trees and protein structure dendrograms. This new phylogeny suggests an APOD-like common ancestor in early chordates, which gave rise, via whole-genome or tandem duplications, to the six Lipocalins currently present in fish (APOD, RBP4, PTGDS, AMBP, C8G, and APOM). Further gene duplications of APOM and PTGDS resulted in the altogether 15 Lipocalins found in contemporary mammals. Insights into the functional impact of relevant amino acid residues in early diverging Lipocalins are also discussed. These results should foster the experimental exploration of novel functions alongside the identification of new members of the Lipocalin family.

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