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.

A consensus amino-acid sequence repeat in Torpedo and mammalian Ca2+-dependent membrane-binding proteins

Nature ◽  
1986 ◽  
Vol 320 (6063) ◽  
pp. 636-638 ◽  
Author(s):  
Michael J. Geisow ◽  
Ulrich Fritsche ◽  
J. Mark Hexham ◽  
Bret Dash ◽  
Tolu Johnson
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Binding Proteins ◽  
Membrane Binding ◽  
Sequence Repeat ◽  
Consensus Amino Acid Sequence ◽  
Consensus Amino Acid

scholarly journals Peptidase E, a Peptidase Specific for N-Terminal Aspartic Dipeptides, Is a Serine Hydrolase

2000 ◽  
Vol 182 (9) ◽  
pp. 2536-2543 ◽  
Author(s):  
Rachel A. L. Lassy ◽  
Charles G. Miller
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Site Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Serine Hydrolase ◽  
Genome Sequences ◽  
New Family ◽  
The Family ◽  
Serovar Typhimurium ◽  
Structural Classes

ABSTRACT Salmonella enterica serovar Typhimurium peptidase E (PepE) is an N-terminal Asp-specific dipeptidase. PepE is not inhibited by any of the classical peptidase inhibitors, and its amino acid sequence does not place it in any of the known peptidase structural classes. A comparison of the amino acid sequence of PepE with a number of related sequences has allowed us to define the amino acid residues that are strongly conserved in this family. To ensure the validity of this comparison, we have expressed one of the most distantly related relatives (Xenopus) in Escherichia coli and have shown that it is indeed an Asp-specific dipeptidase with properties very similar to those of serovar Typhimurium PepE. The sequence comparison suggests that PepE is a serine hydrolase. We have used site-directed mutagenesis to change all of the conserved Ser, His, and Asp residues and have found that Ser120, His157, and Asp135 are all required for activity. Conversion of Ser120 to Cys leads to severely reduced (104-fold) but still detectable activity, and this activity but not that of the parent is inhibited by thiol reagents; these results confirm that this residue is likely to be the catalytic nucleophile. These results suggest that PepE is the prototype of a new family of serine peptidases. The phylogenetic distribution of the family is unusual, since representatives are found in eubacteria, an insect (Drosophila), and a vertebrate (Xenopus) but not in the Archaea or in any of the other eukaryotes for which genome sequences are available.

scholarly journals Genetic and Biochemical Characterization of OXA-535, a Distantly Related OXA-48-Like β-Lactamase

2018 ◽  
Vol 62 (10) ◽  
Author(s):  
L. Dabos ◽  
A. B. Jousset ◽  
R. A. Bonnin ◽  
N. Fortineau ◽  
A. Zavala ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Amino Acid Sequence Identity ◽  
Biochemical Characterization ◽  
Content Type ◽  
Sequence Identity

ABSTRACT OXA-535 is a chromosome-encoded carbapenemase of Shewanella bicestrii JAB-1 that shares only 91.3% amino acid sequence identity with OXA-48. Catalytic efficiencies are similar to those of OXA-48 for most β-lactams, except for ertapenem, where a 2,000-fold-higher efficiency was observed with OXA-535. OXA-535 and OXA-436, a plasmid-encoded variant of OXA-535 differing by three amino acids, form a novel cluster of distantly related OXA-48-like carbapenemases. Comparison of blaOXA-535 and blaOXA-436 genetic environments suggests that an ISCR1 may be responsible for blaOXA-436 gene mobilization from the chromosome of Shewanella spp. to plasmids.

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

Amino acid sequence of .kappa.-flavitoxin: establishment of a new family of snake venom neurotoxins

Biochemistry ◽  
1988 ◽  
Vol 27 (10) ◽  
pp. 3794-3798 ◽  
Author(s):  
Gregory A. Grant ◽  
Mark W. Frazier ◽  
Vincent A. Chiappinelli
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Snake Venom ◽  
New Family

scholarly journals Substrate-binding domains of glycanases from Streptomyces lividans: characterization of a new family of xylan-binding domains

1998 ◽  
Vol 330 (1) ◽  
pp. 41-45 ◽  
Author(s):  
Claude DUPONT ◽  
Martin ROBERGE ◽  
François SHARECK ◽  
Rolf MOROSOLI ◽  
Dieter KLUEPFEL
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Substrate Binding ◽  
Streptomyces Lividans ◽  
Cellulose Binding Domain ◽  
Binding Domains ◽  
New Family ◽  
Cellulose Binding ◽  
Sequence Similarities

The substrate-binding domains of six glycanases from Streptomyces lividans were investigated to determine their specificity towards cellulose and xylan. Based upon amino acid sequence similarities, four of the six domains could be assigned to existing cellulose-binding domain families. However, the binding domains of xylanase A and arabinofuranosidase B could not be classified in any of the known families and should therefore be classified as members of a new family. Evidence is also presented that this new family is one of true xylan-binding domains.

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