Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.34 kDa 
• Atom Count: 7957 
• Modelled Residue Count: 940 
• Deposited Residue Count: 1028 
• Unique protein chains: 1

4OBX

Crystal structure of yeast Coq5 in the apo form

• DOI: 10.2210/pdb4OBX/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-01-07 Released: 2014-08-06 
• Deposition Author(s): Dai, Y.N., Zhou, K., Cao, D.D., Jiang, Y.L., Meng, F., Chi, C.B., Ren, Y.M., Chen, Y.X., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway.

Dai, Y.N., Zhou, K., Cao, D.D., Jiang, Y.L., Meng, F., Chi, C.B., Ren, Y.M., Chen, Y., Zhou, C.Z.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2085-2092

• PubMed: 25084328 
• DOI: 10.1107/S1399004714011559
• Primary Citation of Related Structures:  
  4OBW, 4OBX


• PubMed Abstract: 
  

Saccharomyces cerevisiae Coq5 is an S-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the only C-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2 Å resolution and in the SAM-bound form (Coq5-SAM) at 2.4 Å resolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2 enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule.

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial	A, D [auth B], C, B [auth D]	257	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: COQ5, DBI56, YM8339.09C, YML110C EC: 2.1.1.201
Find proteins for P49017 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49017  Go to UniProtKB:  P49017

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAM	E [auth A], F [auth C]	TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.27	α = 90
b = 75.64	β = 90.85
c = 84.48	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-07 
• Released Date: 2014-08-06 
Deposition Author(s): Dai, Y.N., Zhou, K., Cao, D.D., Jiang, Y.L., Meng, F., Chi, C.B., Ren, Y.M., Chen, Y.X., Zhou, C.Z.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Database references