title: Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach.
abstract: BACKGROUND
  The post-genomic era poses several challenges. The biggest is the identification of biochemical function for protein sequences and structures resulting from genomic initiatives. Most sequences lack a characterized function and are annotated as hypothetical or uncharacterized. While homology-based methods are useful, and work well for sequences with sequence identities above 50%, they fail for sequences in the twilight zone (<30%) of sequence identity. For cases where sequence methods fail, structural approaches are often used, based on the premise that structure preserves function for longer evolutionary time-frames than sequence alone. It is now clear that no single method can be used successfully for functional inference. Given the growing need for functional assignments, we describe here a systematic new approach, designated ligand-centric, which is primarily based on analysis of ligand-bound/unbound structures in the PDB. Results of applying our approach to S-adenosyl-L-methionine (SAM) binding proteins are presented.
  
  
  RESULTS
  Our analysis included 1,224 structures that belong to 172 unique families of the Protein Information Resource Superfamily system. Our ligand-centric approach was divided into four levels: residue, protein/domain, ligand, and family levels. The residue level included the identification of conserved binding site residues based on structure-guided sequence alignments of representative members of a family, and the identification of conserved structural motifs. The protein/domain level included structural classification of proteins, Pfam domains, domain architectures, and protein topologies. The ligand level included ligand conformations, ribose sugar puckering, and the identification of conserved ligand-atom interactions. The family level included phylogenetic analysis.
  
  
  CONCLUSIONS
  We found that SAM bound to a total of 18 different fold types (I-XVIII). We identified 4 new fold types and 11 additional topological arrangements of strands within the well-studied Rossmann fold Methyltransferases (MTases). This extends the existing structural classification of SAM binding proteins. A striking correlation between fold type and the conformation of the bound SAM (classified as types) was found across the 18 fold types. Several site-specific rules were created for the assignment of functional residues to families and proteins that do not have a bound SAM or a solved structure.
authors.affiliation: Department of Biostatistics and Bioinformatics, Georgetown University Medical Center, Washington, DC 20007, USA.
authors.forename: Rajaram
authors.initials: R
authors.lastname: Gana
authors.forename: Shruti
authors.initials: S
authors.lastname: Rao
authors.forename: Hongzhan
authors.initials: H
authors.lastname: Huang
authors.forename: Cathy
authors.initials: C
authors.lastname: Wu
authors.forename: Sona
authors.initials: S
authors.lastname: Vasudevan
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D030562:Databases, Protein; D008024:Ligands; D008780:Methyltransferases / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012436:S-Adenosylmethionine / Q000737:chemistry / Q000378:metabolism*; D013696:Temperature
chemical_list: D008024:Ligands; D011506:Proteins; D012436:S-Adenosylmethionine; D008780:Methyltransferases