Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2.

PubWeight™: 0.78‹?›

🔗 View Article (PMID 26160170)

Published in J Biol Chem on July 09, 2015

Authors

Richard McLean1, Joanne K Hobbs2, Michael D Suits3, Sami T Tuomivaara4, Darryl R Jones1, Alisdair B Boraston2, D Wade Abbott5

Author Affiliations

1: From the Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada.
2: the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada.
3: the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8W 3P6, Canada, the Department of Chemistry and Biochemistry, Wilfred Laurier University, Waterloo, Ontario N2L 3C5, Canada, and.
4: the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602.
5: From the Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada, wade.abbott@agr.gc.ca.

Articles cited by this

MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (2003) 130.85

Features and development of Coot. Acta Crystallogr D Biol Crystallogr (2010) 89.46

XDS. Acta Crystallogr D Biol Crystallogr (2010) 67.46

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37

MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36

Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins (2003) 32.38

Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr (2004) 31.52

jModelTest 2: more models, new heuristics and parallel computing. Nat Methods (2012) 27.83

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (2012) 26.90

Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene (1989) 23.74

Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr (2006) 16.41

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol (2007) 14.96

REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. Acta Crystallogr D Biol Crystallogr (2004) 14.28

The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res (2013) 10.24

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res (2010) 9.68

ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68

dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res (2012) 4.91

Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel (2006) 4.13

Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem J (1997) 3.82

Geometry of metal-ligand interactions in proteins. Acta Crystallogr D Biol Crystallogr (2001) 3.20

The structure, function, and biosynthesis of plant cell wall pectic polysaccharides. Carbohydr Res (2009) 3.08

Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol (2012) 2.54

Maintenance of intracellular calcium in Escherichia coli. J Biol Chem (1987) 1.88

A hierarchical classification of polysaccharide lyases for glycogenomics. Biochem J (2010) 1.87

Completion of autobuilt protein models using a database of protein fragments. Acta Crystallogr D Biol Crystallogr (2012) 1.68

Metal import through microbial membranes. Cell (2004) 1.60

Consolidation of glycosyl hydrolase family 30: a dual domain 4/7 hydrolase family consisting of two structurally distinct groups. FEBS Lett (2010) 1.43

Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology (2004) 1.42

Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology (2010) 1.42

Phylogeny-aware alignment with PRANK. Methods Mol Biol (2014) 1.21

The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family. J Biol Chem (2001) 1.12

Structural biology of pectin degradation by Enterobacteriaceae. Microbiol Mol Biol Rev (2008) 1.10

Vibrio vulnificus: death on the half shell. A personal journey with the pathogen and its ecology. Microb Ecol (2012) 1.09

The exopolygalacturonate lyase PelW and the oligogalacturonate lyase Ogl, two cytoplasmic enzymes of pectin catabolism in Erwinia chrysanthemi 3937. J Bacteriol (1999) 1.08

Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci U S A (2002) 1.05

Identification and characterization of a novel periplasmic polygalacturonic acid binding protein from Yersinia enterolitica. J Mol Biol (2007) 1.03

Calcium at the cell wall-cytoplast interface. J Integr Plant Biol (2010) 1.01

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species. Bioinformatics (2014) 1.00

Using structure to inform carbohydrate binding module function. Curr Opin Struct Biol (2014) 0.94

A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination. J Biol Chem (2007) 0.94

The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination. J Biol Chem (2010) 0.91

The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase. J Mol Biol (2007) 0.90

Structure of a pectin methylesterase from Yersinia enterocolitica. Acta Crystallogr Sect F Struct Biol Cryst Commun (2012) 0.87

Structural determinants responsible for substrate recognition and mode of action in family 11 polysaccharide lyases. J Biol Chem (2009) 0.83

Structure of the oligogalacturonate-specific KdgM porin. Acta Crystallogr D Biol Crystallogr (2014) 0.82

Calciomics: prediction and analysis of EF-hand calcium binding proteins by protein engineering. Sci China Chem (2010) 0.80

An ancestral member of the polysaccharide lyase family 2 displays endolytic activity and magnesium dependence. Appl Biochem Biotechnol (2013) 0.76