2BD1
A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2
Summary for 2BD1
| Entry DOI | 10.2210/pdb2bd1/pdb |
| Related | 1MKT 1UNE 1VL9 2BCH |
| Descriptor | Phospholipase A2, CALCIUM ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (4 entities in total) |
| Functional Keywords | alpha helix, beta sheet, hydrolase |
| Biological source | Bos taurus (cattle) |
| Cellular location | Secreted: P00593 |
| Total number of polymer chains | 2 |
| Total formula weight | 28033.79 |
| Authors | Sekar, K.,Velmurugan, D.,Tsai, M.D. (deposition date: 2005-10-19, release date: 2006-07-04, Last modification date: 2024-10-30) |
| Primary citation | Sekar, K.,Yogavel, M.,Kanaujia, S.P.,Sharma, A.,Velmurugan, D.,Poi, M.J.,Dauter, Z.,Tsai, M.D. Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A(2). Acta Crystallogr.,Sect.D, 62:717-724, 2006 Cited by PubMed Abstract: The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented. PubMed: 16790927DOI: 10.1107/S0907444906014855 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
Download full validation report
