Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database.
The study of mechanistically diverse enzyme superfamilies-collections of enzymes that perform different overall reactions but share both a common fold and a distinct mechanistic step performed by key conserved residues-helps elucidate the structure-function relationships of enzymes. We have developed a resource, the structure-function linkage database (SFLD), to analyze these structure-function relationships. Unique to the SFLD is its hierarchical classification scheme based on linking the specific partial reactions (or other chemical capabilities) that are conserved at the superfamily, subgroup, and family levels with the conserved structural elements that mediate them. We present the results of analyses using the SFLD in correcting misannotations, guiding protein engineering experiments, and elucidating the function of recently solved enzyme structures from the structural genomics initiative. The SFLD is freely accessible at http://sfld.rbvi.ucsf.edu.
Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143-2250, USA.
Scott C-H
SC
Pegg
Shoshana D
SD
Brown
Sunil
S
Ojha
Jennifer
J
Seffernick
Elaine C
EC
Meng
John H
JH
Morris
Patricia J
PJ
Chang
Conrad C
CC
Huang
Thomas E
TE
Ferrin
Patricia C
PC
Babbitt
D000818:Animals; D019295:Computational Biology; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D015202:Protein Engineering / Q000379:methods; D013329:Structure-Activity Relationship
D004798:Enzymes