PDBsum entry 4hgc

Hydrolase/hydrolase inhibitor

PDB id: 4hgc

Contents

Protein chains

223 a.a.

12 a.a.

Ligands

GOL ×5

SO4 ×3

Metals

_CA

Waters ×296

PDB id:

4hgc

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of bovine trypsin complexed with sfti-1 analog containing a peptoid residue at position p1

Structure:

Cationic trypsin. Chain: a. Fragment: unp residues 24-246. Synonym: beta-trypsin, alpha-trypsin chain 1, alpha-trypsin chain 2. Trypsin inhibitor 1. Chain: i. Fragment: unp residues 40-53. Synonym: sfti-1. Engineered: yes

Source:

Bos taurus. Cow. Organism_taxid: 9913. Synthetic: yes. Helianthus annuus. Common sunflower. Organism_taxid: 4232

Resolution:

1.29Å R-factor: 0.127 R-free: 0.157

Authors:

S.Krzywda,M.Jaskolski,K.Rolka,M.Stawikowski

Key ref:

S.Krzywda et al. (2014). Structure of a proteolytically resistant analogue of (NLys)5SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease-mediated proteolysis. Acta Crystallogr D Biol Crystallogr, 70, 668-675. PubMed id: 24598736 DOI: 10.1107/S1399004713032252

Date:

08-Oct-12 Release date: 09-Oct-13

Protein chain

P00760  (TRY1_BOVIN) -  Serine protease 1 from Bos taurus

Seq: 246 a.a.

Struc: 223 a.a.

Protein chain

Q4GWU5  (SFTI1_HELAN) -  Trypsin inhibitor 1 from Helianthus annuus

Seq: 56 a.a.

Struc: 12 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

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

DOI no: 10.1107/S1399004713032252

Acta Crystallogr D Biol Crystallogr 70:668-675 (2014)

PubMed id: 24598736

Structure of a proteolytically resistant analogue of (NLys)5SFTI-1 in complex with trypsin: evidence for the direct participation of the Ser214 carbonyl group in serine protease-mediated proteolysis.

S.Krzywda, M.Jaskolski, K.Rolka, M.J.Stawikowski.

ABSTRACT

Peptide-peptoid hybrids are found to be potent inhibitors of serine proteases. These engineered peptidomimetics benefit from both types of units of the biopolymeric structure: the natural inhibitor part serves as a good binding template, while the P1-positioned peptoid component provides complete resistance towards proteolysis. In this report, the mechanism of proteolytic resistance of a P1 peptoid-containing analogue is postulated based on the crystal structure of the (NLys)(5)-modified sunflower trypsin inhibitor SFTI-1 in complex with bovine trypsin solved at 1.29 Å resolution. The structural differences between the (NLys)(5)SFTI-1-trypsin complex and the native SFTI-1-trypsin complex are surprisingly small and reveal the key role of the carbonyl group of the Ser214 residue of the enzyme, which is crucial for binding of the inhibitor and plays a crucial role in proteolysis mediated by serine proteases. The incorporated NLys5 peptoid residue prevents Ser214 from forming a hydrogen bond to the P1 residue, and in turn Gln192 does not form a hydrogen bond to the carbonyl group of the P2 residue. It also increases the distance between the Ser214 carbonyl group and the Ser195 residue, thus preventing proteolysis. The hybrid inhibitor structure reported here provides insight into protein-protein interaction, which can be efficiently and selectively probed with the use of peptoids incorporated within endogenous peptide ligands.