PDBsum entry 1khq

Hydrolase/hydrolase inhibitor

PDB id: 1khq

Contents

Protein chain

212 a.a. *

Ligands

LEU-PHE-GLY-0HQ

Waters ×105

* Residue conservation analysis

PDB id:

1khq

Name:

Hydrolase/hydrolase inhibitor

Title:

Orthorhombic form of papain/zlfg-dam covalent complex

Structure:

Papain. Chain: a. Fragment: papain, residues 134-345. Synonym: papaya proteinase i, ppi. Peptidic inhibitor. Chain: i. Engineered: yes

Source:

Carica papaya. Papaya. Organism_taxid: 3649. Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.149 R-free: 0.169

Authors:

R.Janowski,M.Kozak,E.Jankowska,Z.Grzonka,M.Jaskolski

Key ref:

R.Janowski et al. (2004). Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor. J Pept Res, 64, 141-150. PubMed id: 15357669

Date:

30-Nov-01 Release date: 09-Sep-03

Protein chain

P50870  (VATD_ENTFC) -  Streptogramin A acetyltransferase from Enterococcus faecium

Seq: 209 a.a.

Struc: 212 a.a.*

* PDB and UniProt seqs differ at 98 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.22.2 - papain.
• Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, with preference for a residue bearing a large hydrophobic sidechain at the P2 position. Does not accept Val at P1'.

J Pept Res 64:141-150 (2004)

PubMed id: 15357669

Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor.

R.Janowski, M.Kozak, E.Jankowska, Z.Grzonka, M.Jaskólski.

ABSTRACT

The three-dimensional structure of two polymorphs of a ZLFG-CH2-papain covalent complex has been determined by X-ray crystallography. The structures indicate that: (i) the methylene carbon atom of the inhibitor is covalently bound to the Sgamma atom of Cys25 of papain; (ii) the hydrophobic S2 pocket formed by Pro68, Val133, Val157, and Asp158 is occupied by the inhibitor's phenylalanyl P2 side chain; (iii) extensive hydrogen bonding and hydrophobic interactions are responsible for the interaction of the inhibitor with the enzyme. Comparison with similar structures suggests that in covalent complexes preservation of main chain-main chain interactions between the enzyme and the inhibitor may have higher priority than the P-S interactions.