PDBsum entry 1o2q

Hydrolase

PDB id: 1o2q

Contents

Protein chain

223 a.a. *

Ligands

SO4

991

Metals

_CA

Waters ×711

* Residue conservation analysis

PDB id:

1o2q

Name:

Hydrolase

Title:

Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors

Structure:

Beta-trypsin. Chain: a. Ec: 3.4.21.4

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas

Resolution:

1.50Å R-factor: 0.177 R-free: 0.188

Authors:

B.A.Katz,K.Elrod,E.Verner,R.L.Mackman,C.Luong,W.D.Shrader,M.Sendzik, J.R.Spencer,P.A.Sprengeler,A.Kolesnikov,V.W.Tai,H.C.Hui, J.G.Breitenbucher,D.Allen,J.W.Janc

Key ref:

B.A.Katz et al. (2003). Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. J Mol Biol, 329, 93. PubMed id: 12742021 DOI: 10.1016/S0022-2836(03)00399-1

Date:

06-Mar-03 Release date: 02-Sep-03

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: 10.1016/S0022-2836(03)00399-1

J Mol Biol 329:93 (2003)

PubMed id: 12742021

Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors.

B.A.Katz, K.Elrod, E.Verner, R.L.Mackman, C.Luong, W.D.Shrader, M.Sendzik, J.R.Spencer, P.A.Sprengeler, A.Kolesnikov, V.W.Tai, H.C.Hui, J.G.Breitenbucher, D.Allen, J.W.Janc.

ABSTRACT

An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog.Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (>11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.

Selected figure(s)

Figure 4.
Figure 4. (a) Resonance forms (A, B) for the lowest energy (non-bind- ing) conformation of the benzi- midazole scaffold. Structure C represents the conformer and tauto- mer for bound benzimidazoles. (b1) Resonance forms for the lowest energy (non-binding) conformation of the 6-chlorobenzimidazole scaffold (D, E). Structure F rep- resents the conformer and tautomer for bound 6-chlorobenzimidazoles. (b2) Resonance forms for bound 6-chlorobenzimidazoles.

Figure 10.
Figure 10. (a) Structure and (2lF ol 2 lFc l); ac map for trypsin-CRA-18306, pH 7.2, 1.56 A š resolution. The OSer195 g -- Ophenol hydrogen bond is short (2.35 ^ 05 A š ) at pH , 7.7 and longer at pH . 7.8 (2.59 ^ 09 A š , Table S1). (b) Structure and (2lF o l 2 lFcl); ac map for trypsin-CRA-18607, pH 7.9, 1.55 A š resolution. Hydrogen bonds (short and ordinary) cor- responding to the (Ooxy, OSer195 (conformation 1) g , Ophenol) array are cyan, while those for the (OS2, OSer195 (conformation 2) g , Ophenol) array are yellow, (or olive green for NHis57 12 -- OS2).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 329, 93-0) copyright 2003.

Figures were selected by an automated process.