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: 27.42 kDa 
• Atom Count: 1718 
• Residue Count: 217 
• Unique protein chains: 1

4KDC

Crystal Structure of UBIG

• DOI: 10.2210/pdb4KDC/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-24 Released: 2014-04-30 
• Deposition Author(s): Zhu, Y., Teng, M., Li, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.225 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Structural and biochemical studies reveal UbiG/Coq3 as a class of novel membrane-binding proteins.

Zhu, Y., Wu, B., Zhang, X., Fan, X., Niu, L., Li, X., Wang, J., Teng, M.

(2015) Biochem J 470: 105-114

• PubMed: 26251450 
• DOI: 10.1042/BJ20150329
• Primary Citation of Related Structures:  
  4KDC


• PubMed Abstract: 
  

UbiG and Coq3 (orthologue in eukaryotes) are SAM-MTases (S-adenosylmethionine-dependent methyltransferases) that catalyse both O-methylation steps in CoQ biosynthesis from prokaryotes to eukaryotes. However, the detailed molecular mechanism by which they function remains elusive. In the present paper, we report that UbiG/Coq3 defines a novel class of membrane-binding proteins. Escherichia coli UbiG binds specifically to liposomes containing PG (phosphatidylglycerol) or CL (cardiolipin, or diphosphatidylglycerol), two major lipid components of the E. coli plasma membrane, whereas human and yeast Coq3 display a strong preference for liposomes enriched with CL, a signature lipid of the mitochondrial membrane. The crystal structure of UbiG from E. coli was determined at 2.1 Å (1 Å = 0.1 nm) resolution. The structure exhibits a typical Class I SAM-MTase fold with several variations, including a unique insertion between strand β5 and helix α10. This insertion is highly conserved and is required for membrane binding. Mutation of the key residues renders UbiG unable to efficiently bind liposome in vitro and the mutant fails to rescue the phenotype of ΔubiG strain in vivo. Taken together, our results shed light on a novel biochemical function of the UbiG/Coq3 protein.

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-demethylubiquinone-9 3-methyltransferase	A	246	Escherichia coli K-12	Mutation(s): 0  Gene Names: ubiG, pufX, yfaB, b2232, JW2226 EC: 2.1.1.64 (PDB Primary Data), 2.1.1.222 (PDB Primary Data)
Find proteins for P17993 (Escherichia coli (strain K12)) Explore P17993  Go to UniProtKB:  P17993

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.225 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.848	α = 90
b = 58.584	β = 105.26
c = 40.168	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-24 
• Released Date: 2014-04-30 
Deposition Author(s): Zhu, Y., Teng, M., Li, X.

Revision History 

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references