PDBsum entry 6t5w

Hydrolase

PDB id: 6t5w

Contents

Protein chain

223 a.a.

Ligands

DMS

SO4

J5K

Metals

_CA

Waters ×201

PDB id:

6t5w

Name:

Hydrolase

Title:

Cationic trypsin in complex with a d-phe-pro-p-aminopyridine derivative (cocrystallizaton at 291 k)

Structure:

Cationic trypsin. Chain: a. Ec: 3.4.21.4

Source:

Bos taurus. Cattle. Organism_taxid: 9913

Resolution:

1.13Å R-factor: 0.129 R-free: 0.145

Authors:

K.Ngo,A.Heine,G.Klebe

Key ref:

K.Ngo et al. (2020). Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? J Med Chem, 63, 3274-3289. PubMed id: 32011145 DOI: 10.1021/acs.jmedchem.9b02061

Date:

17-Oct-19 Release date: 13-May-20

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.21.4 - trypsin.
• Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

DOI no: 10.1021/acs.jmedchem.9b02061

J Med Chem 63:3274-3289 (2020)

PubMed id: 32011145

Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?

K.Ngo, C.Collins-Kautz, S.Gerstenecker, B.Wagner, A.Heine, G.Klebe.

ABSTRACT

Trypsin and thrombin, structurally similar serine proteases, recognize different substrates; thrombin cleaves after Arg, whereas trypsin cleaves after Lys/Arg. Both recognize basic substrate headgroups via Asp189 at the bottom of the S1 pocket. By crystallography and isothermal titration calorimetry (ITC), we studied a series of d-Phe/d-DiPhe-Pro-(amino)pyridines. Identical ligand pairs show the same binding poses. Surprisingly, one ligand binds to trypsin in protonated state and to thrombin in unprotonated state at P1 along with differences in the residual solvation pattern. While trypsin binding is mediated by an ordered water molecule, in thrombin, water is scattered over three hydration sites. Although having highly similar S1 pockets, our results suggest different electrostatic properties of Asp189 possibly contributing to the selectivity determinant. Thrombin binds a specific Na⁺ ion next to Asp189, which is absent in trypsin. The electrostatic properties across the S1 pocket are further attenuated by charged Glu192 at the rim of S1 in thrombin, which is replaced by uncharged Gln192 in trypsin.