Genome-wide analysis of enzyme structure-function combination across three domains of life.
To investigate diverse enzyme structure-function combination (SFC) types in different species, 34 different genome sequences were annotated using the protein catalytic domain database SCOPEC (http://www.enzome.com/enzome/), in which both the structure and function for each entry are known. Annotated enzymes with catalytic domains from the same SCOP superfamily are considered to have an identical structure. Annotated enzymes sharing the identical three-digit EC number are considered to have the same enzymatic function. Results reveal that the different SFC types for enzymes identified in archaea, bacteria and eukaryota are 137, 300 and 313, respectively. About 80% of the SFCs identified in archaea can be consistently found in bacteria and eukaryota species, whereas 28% and 35% combination types in bacteria and eukaryota respectively are unique to their corresponding groups. The number of functions per structure and the number of structures per function for the annotated sequences were measured in different species. Furthermore, a new concept was proposed to represent enzymatic structures as a functional similarity network. Thus, the current study will be helpful to enhance the global view on the evolution of enzymatic structure and function.
Zhang
Ziding
Z
Bioinformatics Center, College of Biological Sciences, China Agricultural University, Beijing 100094, China. zidingzhang@cau.edu.cn
Tang
Yu-Rong
YR
D000818:Animals; D001105:Archaea / Q000201:enzymology* / Q000235:genetics; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D002874:Chromosome Mapping; D030541:Databases, Genetic; D004798:Enzymes / Q000737:chemistry* / Q000235:genetics* / Q000502:physiology*; D005057:Eukaryotic Cells / Q000201:enzymology*; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA; D013329:Structure-Activity Relationship
D004798:Enzymes