Abstract
Luciferases, aryl- and fatty-acyl CoA synthetases, and non-ribosomal peptide synthetase proteins belong to the class I adenylate-forming enzyme superfamily. The reaction catalyzed by the adenylate-forming enzymes is categorized by a two-step process of adenylation and thioesterification. Although all of these proteins perform a similar two-step process, each family may perform the process to yield completely different results. For example, luciferase proteins perform adenylation and oxidation to produce the green fluorescent light found in fireflies, while fatty-acyl CoA synthetases perform adenylation and thioesterification with coenzyme A to assist in metabolic processes involving fatty acids. This study aligned a total of 374 sequences belonging to the adenylate-forming superfamily. Analysis of the sequences revealed five fully conserved residues throughout all sequences, as well as 78 more residues conserved in at least 60% of sequences aligned. Conserved positions are involved in magnesium and AMP binding and maintaining enzyme structure. Also, ten conserved sequence motifs that included most of the conserved residues were identified. A phylogenetic tree was used to assign sequences into nine different groups. Finally, group entropy analysis identified novel conservations unique to each enzyme group. Common group-specific positions identified in multiple groups include positions critical to coordinating AMP and the CoA-bound product, a position that governs active site shape, and positions that help to maintain enzyme structure through hydrogen bonds and hydrophobic interactions. These positions could serve as excellent targets for future research.
Highlights
Class I adenylate-forming enzymes include aryl- and acyl-CoA synthetases, fatty acid-AMP ligases, methylmalonyl-CoA synthetases, the adenylation domain of non-ribosomal peptide synthetases, and luciferases
The project initially began by obtaining the amino acid sequences and tertiary structures of Luciola cruciata luciferase (PDB ID: 2D1R), Brevibacillus brevis gramicidin synthase phenylalanineactivating domain (PDB ID: 1AMU), Thermus thermophilus long chain fatty acyl-CoA synthetase (PDB ID: 1V25), human medium chain fatty acyl-CoA synthetase (PDB ID: 2WD9 & 3DAY), Alcaligenes 4-chlorobenzoyl:CoA ligase (CBL, PDB ID: 3CW9), Salmonella enterica acetyl-CoA synthetase (PDB ID: 1PG3), Rhodopseudomonas palustris methylmalonyl-CoA synthetase (PDB ID: 4FUQ), Methanosarcina acetivorans acyl-adenylate synthetase (PDB ID: 3ETC), Legionella pneumophila fatty acid-AMP ligase (PDB ID: 3KXW), E. coli fatty acid-AMP ligase (PDB ID: 3PBK), Acinetobacter baumannii BasE (PDB ID: 3O82) and Mycobacterium tuberculosis FadD10 long chain fatty acyl-CoA ligase (PDB ID: 4IR7) from the RCSB Protein Data Bank
Five residue positions were invariant among all 374 sequences: Glu328{490}, Gly384{573}, Asp418{624}, Arg433{639} and Lys524{740} (residue positions are in Thermus thermophilus long chain fatty acyl-CoA synthetases (LACSs), unless otherwise noted, with alignment index positions in curly brackets)
Summary
Class I adenylate-forming enzymes ( termed the ANL superfamily [1]) include aryl- and acyl-CoA synthetases, fatty acid-AMP ligases, methylmalonyl-CoA synthetases, the adenylation domain of non-ribosomal peptide synthetases, and luciferases. They represent one class in a superfamily of enzymes that carry out adenylation, the activation of a carboxylate substrate. Analysis of class I adenylate-forming enzymes the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the National Science Foundation grant OCI-1053575. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
