1MEG

CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH E-64

• PDB DOI: https://doi.org/10.2210/pdb1MEG/pdb

• Classification: HYDROLASE
• Organism(s): Carica papaya
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-05-04 Released: 1997-01-11 
• Deposition Author(s): Katerelos, N.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Crystal structure of a caricain D158E mutant in complex with E-64.

Katerelos, N.A., Taylor, M.A., Scott, M., Goodenough, P.W., Pickersgill, R.W.

(1996) FEBS Lett 392: 35-39

• PubMed: 8769310 
• DOI: https://doi.org/10.1016/0014-5793(96)00697-7
• Primary Citation of Related Structures:  
  1MEG


• PubMed Abstract: 
  

  The structure of the D158E mutant of caricain (previously known as papaya protease omega) in complex with E-64 has been determined at 2.0 A resolution (overall R factor 19.3%). The structure reveals that the substituted glutamate makes the same pattern of hydrogen bonds as the aspartate in native caricain. This was not anticipated since in the native structure there is insufficient room to accommodate the glutamate side chain. The glutamate is accommodated in the mutant by a local expansion of the structure demonstrating that small structural changes are responsible for the change in activity.

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Organizational Affiliation: 

Institute of Food Research, Reading Laboratory, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.75 kDa 
• Atom Count: 1,764 
• Modelled Residue Count: 216 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARICAIN	A	216	Carica papaya	Mutation(s): 1  EC: 3.4.22.30
UniProt
Find proteins for P10056 (Carica papaya) Explore P10056  Go to UniProtKB:  P10056

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64	B [auth A]	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O
EOH	C [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.45	α = 90
b = 65.33	β = 111.6
c = 64.37	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-01-11 
Deposition Author(s): Katerelos, N.A.

Revision History  

• Version 1.0: 1997-01-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary