Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.04 kDa 
• Atom Count: 3052 
• Residue Count: 366 
• Unique protein chains: 1

4PMH

The structure of rice weevil pectin methyl esterase

• DOI: 10.2210/pdb4PMH/pdb

• Classification: HYDROLASE
• Organism(s): Sitophilus oryzae
• Expression System: Spodoptera
• Mutation(s): No 


• Deposited: 2014-05-21 Released: 2014-11-12 
• Deposition Author(s): Stenkamp, R.E., Teller, D.C., Behnke, C.A., Reeck, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 

Literature

The structure of rice weevil pectin methylesterase.

Teller, D.C., Behnke, C.A., Pappan, K., Shen, Z., Reese, J.C., Reeck, G.R., Stenkamp, R.E.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1480-1484

• PubMed: 25372813 
• DOI: 10.1107/S2053230X14020433
• Primary Citation of Related Structures:  
  4PMH


• PubMed Abstract: 
  

Rice weevils (Sitophilus oryzae) use a pectin methylesterase (EC 3.1.1.11), along with other enzymes, to digest cell walls in cereal grains. The enzyme is a right-handed β-helix protein, but is circularly permuted relative to plant and bacterial pectin methylesterases, as shown by the crystal structure determination reported here. This is the first structure of an animal pectin methylesterase. Diffraction data were collected to 1.8 Å resolution some time ago for this crystal form, but structure solution required the use of molecular-replacement techniques that have been developed and similar structures that have been deposited in the last 15 years. Comparison of the structure of the rice weevil pectin methylesterase with that from Dickeya dandantii (formerly Erwinia chrysanthemi) indicates that the reaction mechanisms are the same for the insect, plant and bacterial pectin methylesterases. The similarity of the structure of the rice weevil enzyme to the Escherichia coli lipoprotein YbhC suggests that the evolutionary origin of the rice weevil enzyme was a bacterial lipoprotein, the gene for which was transferred to a primitive ancestor of modern weevils and other Curculionidae. Structural comparison of the rice weevil pectin methylesterase with plant and bacterial enzymes demonstrates that the rice weevil protein is circularly permuted relative to the plant and bacterial molecules.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Box 357430, Seattle, WA 98195-7430, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectinesterase	A	366	Sitophilus oryzae	Mutation(s): 0  Gene Names: CE8-1 EC: 3.1.1.11
Find proteins for E7CIP7 (Sitophilus oryzae) Explore E7CIP7  Go to UniProtKB:  E7CIP7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.226 
• R-Value Work: 0.173 
• R-Value Observed: 0.176 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.429	α = 90
b = 73.939	β = 90
c = 204.897	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-21 
• Released Date: 2014-11-12 
Deposition Author(s): Stenkamp, R.E., Teller, D.C., Behnke, C.A., Reeck, G.R.

Revision History 

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy