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Abstract
BackgroundCA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar size in large sequence databases such as UniProt, with pairwise sequence identities in the range of ~40-60%. CA_C2195 was chosen for crystal structure determination for structure-based function annotation of novel protein sequence space.ResultsThe structure confirmed that CA_C2195 contained an N-terminal metallopeptidase-like domain. The structure revealed two extra domains: an α+β domain inserted in the metallopeptidase-like domain and a C-terminal circularly permuted winged-helix-turn-helix domain.ConclusionsBased on our sequence and structural analyses using the crystal structure of CA_C2195 we provide a view into the possible functions of the protein. From contextual information from gene-neighborhood analysis, we propose that rather than being a peptidase, CA_C2195 and its homologs might play a role in biosynthesis of a modified cell-surface carbohydrate in conjunction with several sugar-modification enzymes. These results provide the groundwork for the experimental verification of the function.
Highlights
IntroductionSequence analysis predicted that part of the protein contained a metallopeptidase-related domain
CA_C2195 from Clostridium acetobutylicum is a protein of unknown function
CA_C2195 was targeted by the Joint Center for Structural Genomics (JCSG) in an effort to increase the structural coverage of proteins in Pfam [4] clan CL0035 of metallopeptidases (Peptidase MH/MC/MF), which has ~64000 protein sequences in 12 families (Pfam v27.0, March 2013) but with only limited (~0.2%), biased structural coverage
Summary
Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. CA_C2195 was chosen for crystal structure determination for structure-based function annotation of novel protein sequence space. CA_C2195 from Clostridium acetobutylicum [UniProtKB: Q97H19_CLOAB] is a novel 434-residue protein of unknown function. There are non-peptidase homologs of these proteins: some of these have active catalytic domains, but perform distinct albeit related enzymatic functions, such as the glutaminyl-peptide cyclotransferase. JCSG has determined ~20 structures to date from clan CL0035 (see http://www.topsan.org/ Groups/Zinc_Peptidase). Proteins in these families [7,8] have a broad phylogenetic spread across all kingdoms of life and show substantial sequence divergence
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