title: Structural analysis of papain-like NlpC/P60 superfamily enzymes with a circularly permuted topology reveals potential lipid binding sites.
abstract: NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6) identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.
authors.affiliation: Joint Center for Structural Genomics, La Jolla, California, United States of America.
authors.forename: Qingping
authors.initials: Q
authors.lastname: Xu
authors.forename: Neil D
authors.initials: ND
authors.lastname: Rawlings
authors.forename: Hsiu-Ju
authors.initials: HJ
authors.lastname: Chiu
authors.forename: Lukasz
authors.initials: L
authors.lastname: Jaroszewski
authors.forename: Heath E
authors.initials: HE
authors.lastname: Klock
authors.forename: Mark W
authors.initials: MW
authors.lastname: Knuth
authors.forename: Mitchell D
authors.initials: MD
authors.lastname: Miller
authors.forename: Marc-Andre
authors.initials: MA
authors.lastname: Elsliger
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Deacon
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
mesh_terms: D000595:Amino Acid Sequence; D001409:Bacillus cereus / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D055162:Biocatalysis; D020134:Catalytic Domain; D017124:Conserved Sequence; D005227:Fatty Acids / Q000378:metabolism; D006801:Humans; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D050356:Lipid Metabolism; D008074:Lipoproteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010206:Papain / Q000737:chemistry* / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005227:Fatty Acids; D008024:Ligands; D008074:Lipoproteins; C086389:NlpD protein, bacteria; C116063:P60 protein, bacteria; D010206:Papain