PDBsum entry: 1cqd

Hydrolase

PDB id: 1cqd

Contents

Protein chains

216 a.a. *

Ligands

NAG-FUL-NAG

NAG-NAG

THJ ×4

NAG-FUC-NAG ×2

NAG

NAG-NAG-FUC

Waters ×373

* Residue conservation analysis

PDB id:

1cqd

Name:

Hydrolase

Title:

The 2.1 angstrom structure of a cysteine protease with proli specificity from ginger rhizome, zingiber officinale

Structure:

Protein (protease ii). Chain: a, b, c, d. Other_details: tetrathionate attached to cys-27

Source:

Zingiber officinale. Organism_taxid: 94328. Other_details: purified from ground ginger root

Resolution:

2.10Å R-factor: 0.213 R-free: 0.249

Authors:

K.H.Choi,R.A.Laursen,K.N.Allen

Key ref:

K.H.Choi et al. (1999). The 2.1 A structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale. Biochemistry, 38, 11624-11633. PubMed id: 10512617 DOI: 10.1021/bi990651b

Date:

15-Jun-99 Release date: 28-Sep-99

Protein chains

P82474  (CPGP2_ZINOF) -  Zingipain-2

Seq: 221 a.a.

Struc: 216 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.22.67 - Zingipain.

 Gene Ontology (GO) functional annotation 

• Biological process: proteolysis (1 term)
• Biochemical function: hydrolase activity (4 terms)

DOI no: 10.1021/bi990651b

Biochemistry 38:11624-11633 (1999)

PubMed id: 10512617

The 2.1 A structure of a cysteine protease with proline specificity from ginger rhizome, Zingiber officinale.

K.H.Choi, R.A.Laursen, K.N.Allen.

ABSTRACT

A cysteine protease from ginger rhizome (GP-II) cleaves peptides and proteins with proline at the P(2) position. The unusual specificity for proline makes GP-II an attractive tool for protein sequencing and identification of stably folded domains in proteins. The enzyme is a 221 amino acid glycoprotein possessing two N-linked oligosaccharide chains (8% glycosylated by weight) at Asn99 and Asn156. The availability of the sequence of these glycosyl chains afforded the opportunity to observe their structure and impact on protein conformation. The three-dimensional structure of GP-II has been determined by X-ray crystallography to a resolution of 2.1 A (overall R-factor = 0.214, free R = 0.248). The overall structure of GP-II is similar to that of the homologous cysteine proteases papain, actinidin, and glycyl endopeptidase, folding into two distinct domains of roughly equal size which are divided by a cleft. The observed N-linked glycosyl chains (half the total carbohydrate sequence) participate in both crystallographic and noncrystallographic contacts, tethering the proteins together via hydrogen bonds to the carbohydrate residues without intervening ordered water molecules. The putative S(2) binding pocket (the proline recognition site) was identified by superposition of the GP-II structure with structures of four previously determined papain-inhibitor complexes. The particular enzymic amino acids forming the S(2) pocket of GP-II (Trp, Met, and Ala) are similar to those found in the proline binding pockets of the unrelated enzymes alpha-lytic protease and cyclophilin. However, there is no conserved three-dimensional arrangement of these residues between the three enzymes (i.e., no proline binding motif). Thus, the particular amino acids found at S(2) are consistent with a binding pocket for a moiety with the steric characteristics and charge distribution of proline. Size exclusion is also a mechanism for selectivity compared to the S(2) binding pocket of papain. The S(2) binding pocket of GP-II greatly restricts the size of the side chain which could be bound because of the occurrence of a tryptophan in place of the corresponding tyrosine in papain. In light of the nature of the binding pocket, the specificity of GP-II for proline over other small nonpolar amino acids may be attributed to a direct effect of proline on the substrate peptide backbone conformation.