ISDA

Deposition Date 2010-10-12

Release Date 2010-11-10

Last Version Date 2024-11-06

Entry Detail

PDB ID:

2XTT

Keywords:

HYDROLASE

Title:

Bovine trypsin in complex with evolutionary enhanced Schistocerca gregaria protease inhibitor 1 (SGPI-1-P02)

Biological Source:

Source Organism:

SCHISTOCERCA GREGARIA (Taxon ID: 7010)
BOS TAURUS (Taxon ID: 9913)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

0.93 Å

R-Value Free:

0.13

Space Group:

P 1 21 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEASE INHIBITOR SGPI-1
Chain IDs:A
Chain Length:36
Number of Molecules:1
Biological Source:SCHISTOCERCA GREGARIA

UniProt ID:O46162 Pfam ID:PF05375

Protein Blast

Polymer Type:polypeptide(L)
Molecule:CATIONIC TRYPSIN
Gene (Uniprot):PRSS1
Chain IDs:B
Chain Length:223
Number of Molecules:1
Biological Source:BOS TAURUS

UniProt ID:P00760 Pfam ID:PF00089 EC:3.4.21.4

Ligand Molecules

ACT

Primary Citation

The catalytic aspartate is protonated in the Michaelis complex formed between trypsin and an in vitro evolved substrate-like inhibitor: a refined mechanism of serine protease action.

Wahlgren, W.Y, Pal, G, Kardos, J, Porrogi, P, Szenthe, B, Patthy, A, Graf, L, Katona, G.Show

J.Biol.Chem. 286 3587 3596 (2011)

PMID: 21097875 DOI: 10.1074/jbc.M110.161604

Abstact

The mechanism of serine proteases prominently illustrates how charged amino acid residues and proton transfer events facilitate enzyme catalysis. Here we present an ultrahigh resolution (0.93 Å) x-ray structure of a complex formed between trypsin and a canonical inhibitor acting through a substrate-like mechanism. The electron density indicates the protonation state of all catalytic residues where the catalytic histidine is, as expected, in its neutral state prior to the acylation step by the catalytic serine. The carboxyl group of the catalytic aspartate displays an asymmetric electron density so that the O(δ2)-C(γ) bond appears to be a double bond, with O(δ2) involved in a hydrogen bond to His-57 and Ser-214. Only when Asp-102 is protonated on O(δ1) atom could a density functional theory simulation reproduce the observed electron density. The presence of a putative hydrogen atom is also confirmed by a residual mF(obs) - DF(calc) density above 2.5 σ next to O(δ1). As a possible functional role for the neutral aspartate in the active site, we propose that in the substrate-bound form, the neutral aspartate residue helps to keep the pK(a) of the histidine sufficiently low, in the active neutral form. When the histidine receives a proton during the catalytic cycle, the aspartate becomes simultaneously negatively charged, providing additional stabilization for the protonated histidine and indirectly to the tetrahedral intermediate. This novel proposal unifies the seemingly conflicting experimental observations, which were previously seen as either supporting the charge relay mechanism or the neutral pK(a) histidine theory.

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