2W12

High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding

Summary for 2W12

• Entry DOI: 10.2210/pdb2w12/pdb
• Related: 1ND1 2W13 2W14 2W15
• Descriptor: ZINC METALLOPROTEINASE BAP1, ZINC ION, (2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE, ... (5 entities in total)
• Functional Keywords: hydrolase inhibitor complex, metal-binding, zinc-depending, metalloprotease, metalloproteinase-inhibitor complex, zinc, toxin, secreted, protease, hydrolase, p-i snake venom metalloproteinase, metzincin, chemotaxis, adamalysin, endopeptidase, alpha-beta protein, matrixmetalloproteinase, tumor necrosis factor alpha converting enzyme, pyrrolidone carboxylic acid, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: BOTHROPS ASPER (TERCIOPELO)
• Total number of polymer chains: 1
• Total formula weight: 23383.82

Authors

Lingott, T.J.,Schleberger, C.,Gutierrez, J.M.,Merfort, I. (deposition date: 2008-10-14, release date: 2009-06-16, Last modification date: 2024-11-06)

Primary citation

Lingott, T.J.,Schleberger, C.,Gutierrez, J.M.,Merfort, I.
High-Resolution Crystal Structure of the Snake Venom Metalloproteinase Bap1 Complexed with a Peptidomimetic: Insight Into Inhibitor Binding.
Biochemistry, 48:6166-, 2009

PubMed Abstract: BaP1, a zinc-dependent endopeptidase belonging to the P-I class of snake venom metalloproteinases, exerts multiple tissue-damaging activities, leading to hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. Interestingly, this metalloproteinase shows a high degree of structural homology with the catalytic domain of human adamalysins and matrix metalloproteinases, especially at the strictly conserved zinc binding motif and the so-called Met turn. This highlights BaP1 as an interesting model concerning inhibitor design for several medicinally important metalloproteinases, such as tumor necrosis factor alpha converting enzyme. Here, we report the first crystal structure of BaP1 complexed with a peptidomimetic inhibitor. Suitable crystals were obtained at four different pH values (4.6, 6.5, 7.5, and 8.0), and four high-resolution structures (1.46, 1.14, 1.08, and 1.05 A) were established. These structures and the detailed analysis of the structure-activity relationship of the bound inhibitor form a basis for the design of potent BaP1 inhibitors. The latter can be used for the treatment of local pathological effects caused by snake bites, mainly due to metalloproteinases such as BaP1. Besides, the high-resolution structure is an excellent starting point for the rational development of inhibitors for human metalloproteinases. The finding of a flexible loop region may have a great impact on further studies as to date little is known about the structural dependencies of the hemorrhagic activity of snake venom metalloproteinases.

PubMed: 19485419
DOI: 10.1021/BI9002315

Experimental method

X-RAY DIFFRACTION (1.46 Å)