1WL9

Structure of aminopeptidase P from E. coli

Replaces:  1AZ9

Summary for 1WL9

• Entry DOI: 10.2210/pdb1wl9/pdb
• Related: 1AZ9 1JAW 1M35
• Descriptor: Xaa-Pro aminopeptidase, MANGANESE (II) ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: proline-specific peptidase, metalloenzyme, pita-bread fold, hydrolase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 49905.39

Authors

Graham, S.C.,Bond, C.S.,Freeman, H.C.,Guss, J.M. (deposition date: 2004-06-22, release date: 2005-08-16, Last modification date: 2024-10-09)

Primary citation

Graham, S.C.,Bond, C.S.,Freeman, H.C.,Guss, J.M.
Structural and functional implications of metal ion selection in aminopeptidase p, a metalloprotease with a dinuclear metal center
Biochemistry, 44:13820-13836, 2005

PubMed Abstract: The effect of metal substitution on the activity and structure of the aminopeptidase P (APPro) from Escherichia coli has been investigated. Measurements of activity in the presence of Mn2+, Mg2+, Zn2+, Na+, and Ca2+ show that significant activity is seen only in the Mn-bound form of the enzyme. The addition of Zn2+ to [MnMn(APPro)] is strongly inhibitory. Crystal structures of [MnMn(APPro)], [MgMg(APPro)], [ZnZn(APPro)], [ZnMg(APPro)], [Ca_(APPro)], [Na_(APPro)], and [apo(APPro)] were determined. The structures of [Ca_(APPro)] and [Na_(APPro)] have a single metal atom at their active site. Surprisingly, when a tripeptide substrate (ValProLeu) was soaked into [Na_(APPro)] crystals in the presence of 200 mM Mg2+, the structure had substrate, but no metal, bound at the active site. The structure of apo APPro complexed with ValProLeu shows that the N-terminal amino group of a substrate can be bound at the active site by carboxylate side chains that normally bind the second metal atom, providing a model for substrate binding in a single-metal active enzyme. Structures of [MnMn(APPro)] and [ZnZn(APPro)] complexes of ProLeu, a product inhibitor, in the presence of excess Zn reveal a third metal-binding site, formed by two conserved His residues and the dipeptide inhibitor. A Zn atom bound at such a site would stabilize product binding and enhance inhibition.

PubMed: 16229471
DOI: 10.1021/bi0512849

Experimental method

X-RAY DIFFRACTION (1.9 Å)