1CQD

THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

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

(1999) Biochemistry 38: 11624-11633


  • PubMed 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PROTEASE II)
A, B, C, D
221Zingiber officinaleEC: 3.4.22.67
Find proteins for P82474 (Zingiber officinale)
Go to UniProtKB:  P82474
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
THJ
Query on THJ

Download SDF File 
Download CCD File 
A, B, C, D
THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
A
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 93.980α = 90.00
b = 45.450β = 105.03
c = 110.040γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance