Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III

Abstract

Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is widely distributed in organisms and present in almost all human tissues. In addition to its involvement in protein catabolism, it plays...

Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III

“…In our previous work [ 19 ], we determined the main binding modes of the second zinc ion to hDPP III and traced the exchange of the ion in the additional, inhibitory, binding site with the catalytic ion. In this work, we investigated the binding of Cu ions to hDPP III.…”

“…It has also been shown that the binding of zinc and other metals in excess can lead to the inhibition of DPP III in humans, rats, and microorganisms [ 9 , 10 , 11 ]. All of these findings indicate that metal ions can bind not only at the catalytic site of DPP III, but also at an additional, so-called inhibitory binding site [ 19 , 20 , 21 ].…”

“…There is only one zinc ion in the active site of the crystallographically determined structures of DPP III (PDB IDs of structures of the following: human—3FVY, 3T6B, 3T6J, 5EGY, 5E2Q, 5E33, 5E3A, 5E3C, 5EHH [ 12 , 13 ]; yeast—3CSK [ 14 ], fungal—5YFB, 5YFC, 5YFD [ 15 ]; bacterial DPP III—5NA6, 6NA7, 5NA8, 5ZUM, 6EOM [ 16 , 17 , 18 ]), but previous studies [ 19 , 20 , 21 ] clearly indicated the possibility of another metal-ion binding, which inhibits the enzymatic activity of DPP III. The binding of another metal ion in the so-called inhibitory metal-binding site, which is directly adjacent to the catalytically active site of the enzyme, has been observed in the crystallographic structures of three zinc-dependent enzymes, in which, as in DPP III, the catalytic zinc is coordinated with two histidines and the carboxyl groups of the amino acids Glu or Asp: carboxypeptidase A, thermolysin, and LpxC (the PDB codes of the corresponding structures are 1CPX, 1LND, and 1P42) [ 22 , 23 , 24 ].…”

“…Using the same procedure that Young and Siemann used to determine the potential binding site of the inhibitory Zn 2+ ion in LF, we can determine the binding site of the inhibitory metal in DPP III. We have shown computationally that human DPP III (hDPP III) can take up a second zinc ion that binds immediately next to the catalytically important ion and displaces the zinc in the active site, while the zinc that originally occupied the active site leaves the enzyme [ 19 ].…”

Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates

“…Dipeptidyl-peptidase III (DPP III, EC 3.4.14.4) is a zinc metallopeptidase of the M49 family [1][2][3][4] which participates in the metabolic process in human bodies by cleaving dipeptide from the N-terminal of biologically active oligopeptides such as angiotensin II (Ang II) [4][5][6]. The M49 family (MEROPS, the Peptidase Database) [7] of the DPP III family is defined by five conserved amino acid sequence regions, including the unique hexapeptide zinc-binding motif (HEXXGH).…”