3KW0
Crystal structure of Cysteine peptidase (NP_982244.1) from BACILLUS CEREUS ATCC 10987 at 2.50 A resolution
Summary for 3KW0
| Entry DOI | 10.2210/pdb3kw0/pdb |
| Descriptor | Cysteine peptidase, LYSINE, CHLORIDE ION, ... (4 entities in total) |
| Functional Keywords | cysteine peptidase, structural genomics, joint center for structural genomics, jcsg, protein structure initiative, psi-2, hydrolase |
| Biological source | Bacillus cereus |
| Total number of polymer chains | 4 |
| Total formula weight | 100156.95 |
| Authors | Joint Center for Structural Genomics (JCSG) (deposition date: 2009-11-30, release date: 2009-12-15, Last modification date: 2024-11-20) |
| Primary citation | Xu, Q.,Rawlings, N.D.,Chiu, H.J.,Jaroszewski, L.,Klock, H.E.,Knuth, M.W.,Miller, M.D.,Elsliger, M.A.,Deacon, A.M.,Godzik, A.,Lesley, S.A.,Wilson, I.A. Structural Analysis of Papain-Like NlpC/P60 Superfamily Enzymes with a Circularly Permuted Topology Reveals Potential Lipid Binding Sites. Plos One, 6:e22013-e22013, 2011 Cited by PubMed 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. PubMed: 21799766DOI: 10.1371/journal.pone.0022013 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.5 Å) |
Structure validation
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