The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases

Abstract

Laccases and their homologues form the protein superfamily of multicopper oxidases (MCO). They catalyze the oxidation of many, particularly phenolic substances, and, besides playing an important role in many cellular activities, are of interest in biotechnological applications. The Laccase Engineering Database (LccED, http://www.lcced.uni-stuttgart.de) was designed to serve as a tool for a systematic sequence-based classification and analysis of the diverse multicopper oxidase protein family. More than 2200 proteins were classified into 11 superfamilies and 56 homologous families. For each family, the LccED provides multiple sequence alignments, phylogenetic trees and family-specific HMM profiles. The integration of structures for 14 different proteins allows a comprehensive comparison of sequences and structures to derive biochemical properties. Among the families, the distribution of the proteins regarding different kingdoms was investigated. The database was applied to perform a comprehensive analysis by MCO- and laccase-specific patterns.The LccED combines information of sequences and structures of MCOs. It serves as a classification tool to assign new proteins to a homologous family and can be applied to investigate sequence–structure–function relationship and to guide protein engineering.Database URL: http://www.lcced.uni-stuttgart.de

Characterization of a novel high-pH-tolerant laccase-like multicopper oxidase and its sequence diversity in Thioalkalivibrio sp

“…This prompted a more thorough revision of the diversity and abundance of laccases within the bacterial domain. Recent bioinformatic studies showed that genes for laccase-like enzymes are widely distributed in nearly all bacterial phyla and that the diversity of these enzymes in bacteria may well exceed our expectations (Ausec et al 2011b;Sirim et al 2011).…”

“…Recent reports of highly pH-tolerant bacterial laccases (Reiss et al 2011;Singh et al 2007;Ye et al 2010;Zheng et al 2011;Sondhi et al 2014) highlight the importance of studying these enzymes in more depth. While broad approaches such as metagenomics may prove successful in finding novel laccases (Ye et al 2010), focused bioinformatic studies (Ausec et al 2011b) and on-line databases (Sirim et al 2011) suggested that potentially interesting laccase genes may be mined from putative laccase-encoding organisms.…”

Elimination of Manganese(II,III) Oxidation in Pseudomonas putida GB-1 by a Double Knockout of Two Putative Multicopper Oxidase Genes

“…Why, then, does P. putida GB-1 have two? According to the Laccase Engineering Database (http://www .lcced.uni-stuttgart.de/) (43), McoA belongs to the bilirubin oxidase MCO superfamily, while GB-1 MnxG has a low level of similarity to the small laccase (SLAC) superfamily. Both are predicted to have signal peptides and be exported, but McoA has a putative transmembrane helix, suggesting that it may be membrane bound (http://img.jgi.doe.gov/cgi-bin/w/main.cgi).…”

Structural and functional characterization of two-domain laccase from Streptomyces viridochromogenes

“…Type A 2DLac contain a T1 centre in each cupredoxin domain, whereas a single T1 centre is present in the second or first cupredoxin domain of type B and type C 2DLac, respectively. Analysis of microbial genomes revealed the widespread occurrence of 2DLac enzymes in different groups of bacteria, including bacteria of the genus Streptomyces [16,17]. Despite the prevalence of 2DLac enzymes, their biochemical properties were studied only sparsely, e.g.…”