The Structure–Function Linkage Database

Abstract

The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.

Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus

“…The class I terpene synthases, which are related to polyprenyl diphosphate synthases, have a single all α-helix α-domain (PF03936) and are found mostly in bacteria and fungi. The Structure-Function Linkage Database (SFLD) (26) assigns 931 protein sequences to the class I terpene synthases, which are listed in the "terpene synthase-like 2 subgroup" (26). We constructed sequence similarity networks using these sequences (26).…”

“…The Structure-Function Linkage Database (SFLD) (26) assigns 931 protein sequences to the class I terpene synthases, which are listed in the "terpene synthase-like 2 subgroup" (26). We constructed sequence similarity networks using these sequences (26). At an e-value cutoff of 10 −50 , these enzymes segregate into 14 main clusters containing 10 or more members (Fig.…”

The Radical S-Adenosyl-l-methionine Enzyme QhpD Catalyzes Sequential Formation of Intra-protein Sulfur-to-Methylene Carbon Thioether Bonds

“…The QhpD protein belongs to the radical S-adenosylmethionine (SAM) superfamily currently comprising ϳ113,600 members (9), harboring the consensus CX 3 CX 2 C [4Fe-4S] clusterbinding motif in the N-terminal region (10 -12). QhpD is essential for the biogenesis of QHNDH, most likely by participating in the Cys-to-Asp/Glu thioether bond formation in the ␥ subunit (maturated QhpC) (7).…”

“…According to recent bioinformatics analysis, QhpD is classified into the subgroup "SPASM/ twitch domain-containing," named for its biochemically characterized founding members as follows: subtilosin Asynthesizing enzyme, AlbA; pyrroloquinoline quinone biosynthetic enzyme, PqqE; anaerobic sulfatase-maturating enzyme, anSME; and mycofactocin synthesizing enzyme, MtfC (13,14). About 11,800 members classified into this subgroup (9) are characterized by sharing the 7-cysteine motif (CX 9 -15 GX 4 Cgap-CX 2 CX 5 CX 3 C-gap-C) in the C-terminal half (15), which are likely involved in binding of auxiliary [4Fe-4S] clusters (16,17). Moreover, multiple sequence alignment of QhpD and its homologs with other SPASM proteins ( Fig.…”

“…Moreover, multiple sequence alignment of QhpD and its homologs with other SPASM proteins ( Fig. 2) reveals strict conservation of several residues throughout the subgroup and also some residues only among QhpD homologs that constitute the QHNDH maturation protein family (9), in addition to the N-terminal signature CX 3 CX 2 C motif that ligates the SAMbinding [4Fe-4S] cluster (10 -12). These SPASM proteins are primarily involved in cofactor and peptide maturation processes, acting on ribosomally translated proteins (peptides) encoded in the vicinity of their genes (14).…”