Assignment of enzyme substrate specificity by principal component analysis of aligned protein sequences: An experimental test using DNA glycosylase homologs

We have studied the relationship between amino acid sequence and substrate specificity in a DNA glycosylase family by characterizing experimentally the specificity of four new members of the family. We show that principal component analysis (PCA) of the sequence family correctly predicts the substra...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2000-07, Vol.40 (1), p.98-105
Main Authors: Gogos, Arhonda, Jantz, Derek, Sentürker, Sema, Richardson, Delwood, Dizdaroglu, Miral, Clarke, Neil D.
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Catalytic Domain
Consensus Sequence
DNA glycosylase
DNA Glycosylases
Evolution, Molecular
genome annotation
Humans
Markov Chains
Models, Molecular
Molecular Sequence Data
N-Glycosyl Hydrolases - chemistry
principal component analysis
Protein Structure, Tertiary
Sequence Alignment
Sequence Homology, Amino Acid
Space life sciences
Substrate Specificity
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Summary:We have studied the relationship between amino acid sequence and substrate specificity in a DNA glycosylase family by characterizing experimentally the specificity of four new members of the family. We show that principal component analysis (PCA) of the sequence family correctly predicts the substrate specificity of one of the novel homologs even though conventional sequence analysis methods fail to group this homolog with other sequences of the same specificity. PCA also suggested, correctly, that another homolog characterized previously differs in its specificity from those sequences with which it clusters by conventional criteria. These results suggest that principal component analysis of sequence families can be a useful tool in annotating genome sequences when there is ambiguity concerning which subfamily a new homolog belongs to. Proteins 2000;40:98–105. Published 2000 Wiley‐Liss, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/(SICI)1097-0134(20000701)40:1<98::AID-PROT110>3.0.CO;2-S