PDBsum entry 6t4a

Hydrolase

PDB id: 6t4a

Contents

Protein chains

28 a.a.

251 a.a.

Ligands

ASP-PHE-GLU-GLU-ILE-PRO-GLU-GLU-TYS-LEU

NAG

J5K

PO4

GOL

Metals

_NA ×2

Waters ×262

PDB id:

6t4a

Name:

Hydrolase

Title:

Thrombin in complex with a d-phe-pro-p-aminopyridine derivative

Structure:

Prothrombin. Chain: l. Synonym: coagulation factor ii. Prothrombin. Chain: h. Synonym: coagulation factor ii. Hirudin variant-2. Chain: i. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421

Resolution:

1.31Å R-factor: 0.128 R-free: 0.148

Authors:

K.Ngo,C.Collins,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:

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

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 251 a.a.

Enzyme reactions

• Enzyme class: Chains L, H: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

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.