2XTT

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

Summary for 2XTT

• Entry DOI: 10.2210/pdb2xtt/pdb
• Related: 1AQ7 1AUJ 1AZ8 1BJU 1BJV 1BTP 1BTW 1BTX 1BTY 1BTZ 1C1N 1C1O 1C1P 1C1Q 1C1R 1C1S 1C1T 1C2D 1C2E 1C2F 1C2G 1C2H 1C2I 1C2J 1C2K 1C2L 1C2M 1C5P 1C5Q 1C5R 1C5S 1C5T 1C5U 1C5V 1C9T 1CE5 1CU7 1CU8 1CU9 1D6R 1EB2 1EJM 1EZX 1F0T 1F0U 1F2S 1G36 1G3B 1G3C 1G3D 1G3E 1G9I 1GBT 1GHZ 1GI0 1GI1 1GI2 1GI3 1GI4 1GI5 1GI6 1GJ6 1HJ9 1J8A 1JIR 1JRS 1JRT 1K1I 1K1J 1K1L 1K1M 1K1N 1K1O 1K1P 1KGM 1KIO 1KJ0 1LQE 1MAX 1MAY 1MTS 1MTU 1MTV 1MTW 1N6X 1N6Y 1NC6 1NTP 1O2H 1O2I 1O2J 1O2K 1O2L 1O2M 1O2N 1O2O 1O2P 1O2Q 1O2R 1O2S 1O2T 1O2U 1O2V 1O2W 1O2X 1O2Y 1O2Z 1O30 1O31 1O32 1O33 1O34 1O35 1O36 1O37 1O38 1O39 1O3A 1O3B 1O3C 1O3D 1O3E 1O3F 1O3G 1O3H 1O3I 1O3J 1O3K 1O3L 1O3M 1O3N 1O3O 1OPH 1OX1 1OYQ 1P2I 1P2J 1P2K 1PPC 1PPE 1PPH 1QA0 1QB1 1QB6 1QB9 1QBN 1QBO 1QCP 1QL7 1QL8 1RXP 1S0Q 1S0R 1SBW 1SFI 1SMF 1TAB 1TAW 1TGB 1TGC 1TGN 1TGS 1TGT 1TIO 1TLD 1TNG 1TNH 1TNI 1TNJ 1TNK 1TNL 1TPA 1TPO 1TPP 1TPS 1TX7 1TX8 1TYN 1UTN 1UTO 1UTP 1UTQ 1V2J 1V2K 1V2L 1V2M 1V2N 1V2O 1V2P 1V2Q 1V2R 1V2S 1V2T 1V2U 1V2V 1V2W 1XUF 1XUG 1XUH 1XUI 1XUJ 1XUK 1Y3U 1Y3V 1Y3W 1Y3X 1Y3Y 1Y59 1Y5A 1Y5B 1Y5U 1YP9 1YYY 1ZR0 1ZZZ 2A7H 2AH4 2AYW 2BLV 2BLW 2BTC 2BY5 2BY6 2BY7 2BY8 2BY9 2BYA 2BZA 2CMY 2FI3 2FI4 2FI5 2FTL 2FTM 2FX4 2FX6 2J9N 2PTC 2PTN 2TGA 2TGD 2TGP 2TGT 2TIO 2TLD 2TPI 2UUY 3BTD 3BTE 3BTF 3BTG 3BTH 3BTK 3BTM 3BTQ 3BTT 3BTW 3PTB 3PTN 3TPI 4TPI 5PTP
• Descriptor: PROTEASE INHIBITOR SGPI-1, CATIONIC TRYPSIN, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: hydrolase, catalytic mechanism, inhibition, in vitro evolution
• Biological source: BOS TAURUS (BOVINE); More
• Total number of polymer chains: 2
• Total formula weight: 27355.81

Authors

Wahlgren, W.Y.,Pal, G.,Kardos, J.,Porrogi, P.,Szenthe, B.,Patthy, A.,Graf, L.,Katona, G. (deposition date: 2010-10-12, release date: 2010-11-10, Last modification date: 2024-11-06)

Primary citation

Wahlgren, W.Y.,Pal, G.,Kardos, J.,Porrogi, P.,Szenthe, B.,Patthy, A.,Graf, L.,Katona, G.
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.
J.Biol.Chem., 286:3587-3596, 2011

PubMed Abstract: 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.

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

Experimental method

X-RAY DIFFRACTION (0.93 Å)