PDBsum entry 4kel

Hydrolase/hydrolase inhibitor

PDB id: 4kel

Contents

Protein chains

223 a.a.

14 a.a.

Waters ×209

PDB id:

4kel

Name:

Hydrolase/hydrolase inhibitor

Title:

Atomic resolution crystal structure of kallikrein-related peptidase 4 complexed with a modified sfti inhibitor fcqr(n)

Structure:

Kallikrein-4. Chain: a. Fragment: related peptidase 4, unp residues 31-253. Synonym: enamel matrix serine proteinase 1, kallikrein-like protein 1, klk-l1, prostase, serine protease 17. Engineered: yes. Trypsin inhibitor 1. Chain: b. Synonym: sfti-1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: klk4. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Helianthus annuus. Common sunflower.

Resolution:

1.15Å R-factor: 0.138 R-free: 0.163

Authors:

O.V.Ilyichova,J.E.Swedberg,S.J.De Veer,K.C.Sit,J.M.Harris,A.M.Buckle

Key ref:

B.T.Riley et al. (2019). KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors. Biochemistry, 58, 2524-2533. PubMed id: 31058493 DOI: 10.1021/acs.biochem.9b00191

Date:

25-Apr-13 Release date: 30-Apr-14

Protein chain

Q9Y5K2  (KLK4_HUMAN) -  Kallikrein-4 from Homo sapiens

Seq: 254 a.a.

Struc: 223 a.a.*

Protein chain

Q4GWU5  (SFTI1_HELAN) -  Trypsin inhibitor 1 from Helianthus annuus

Seq: 56 a.a.

Struc: 14 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.21.- - ?????

DOI no: 10.1021/acs.biochem.9b00191

Biochemistry 58:2524-2533 (2019)

PubMed id: 31058493

KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors.

B.T.Riley, O.Ilyichova, S.J.de Veer, J.E.Swedberg, E.Wilson, D.E.Hoke, J.M.Harris, A.M.Buckle.

ABSTRACT

Sunflower trypsin inhibitor (SFTI-1) is a 14 amino acid serine protease inhibitor. The dual antiparallel β-sheet arrangement of SFTI-1 is stabilized by an N-terminal-C-terminal backbone cyclization and a further disulfide bridge to form a final bicyclic structure. This constrained structure is further rigidified by an extensive network of internal hydrogen bonds. Thus, the structure of SFTI-1 in solution resembles the protease-bound structure, reducing the entropic penalty upon protease binding. When cleaved at the scissile bond, it is thought that the rigidifying features of SFTI-1 maintain its structure, allowing the scissile bond to be reformed. The lack of structural plasticity for SFTI-1 is proposed to favor initial protease binding and continued occupancy in the protease active site, resulting in an equilibrium between the cleaved and uncleaved inhibitor in the presence of a protease. We have determined, at 1.15 Å resolution, the X-ray crystal structures of complexes between human kallikrein-related peptidase 4 (KLK4) and SFTI-FCQR(Asn14) and between KLK4 and an acyclic form of the same inhibitor, SFTI-FCQR(Asn14)[1,14], with the latter displaying a cleaved scissile bond. Structural analysis and MD simulations together reveal the roles of the altered contact sequence, intramolecular hydrogen bonding network, and backbone cyclization in altering the state of SFTI's scissile bond ligation at the protease active site. Taken together, the data presented reveal insights into the role of dynamics in the standard-mechanism inhibition and suggest that modifications on the non-contact strand may be a useful, underexplored approach for generating further potent or selective SFTI-based inhibitors against members of the serine protease family.