Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 191.41 kDa 
• Atom Count: 12385 
• Modelled Residue Count: 1571 
• Deposited Residue Count: 1710 
• Unique protein chains: 1

4ELS

Structure of E. Coli. 1,4-dihydroxy-2- naphthoyl coenzyme A synthases (MENB) in complex with bicarbonate

• PDB DOI: 10.2210/pdb4ELS/pdb

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


• Deposited: 2012-04-11 Released: 2012-06-06 
• Deposition Author(s): Sun, Y.R., Song, H.G., Li, J., Jiang, M., Li, Y., Zhou, J.H., Guo, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Active site binding and catalytic role of bicarbonate in 1,4-dihydroxy-2-naphthoyl coenzyme A synthases from vitamin K biosynthetic pathways

Sun, Y.R., Song, H.G., Li, J., Jiang, M., Li, Y., Zhou, J.H., Guo, Z.H.

(2012) Biochemistry 51: 4580-4589

• PubMed: 22606952 
• DOI: 10.1021/bi300486j
• Primary Citation of Related Structures:  
  4ELS, 4ELW, 4ELX, 4EML


• PubMed Abstract: 
  

1,4-Dihydroxy-2-naphthoyl coenzyme A (DHNA-CoA) synthase, or MenB, catalyzes a carbon-carbon bond formation reaction in the biosynthesis of both vitamin K1 and K2. Bicarbonate is crucial to the activity of a large subset of its orthologues but lacks a clearly defined structural and mechanistic role. Here we determine the crystal structure of the holoenzymes from Escherichia coli at 2.30 Å and Synechocystis sp. PCC6803 at 2.04 Å, in which the bicarbonate cofactor is bound to the enzyme active site at a position equivalent to that of the side chain carboxylate of an aspartate residue conserved among bicarbonate-insensitive DHNA-CoA synthases. Binding of the planar anion involves both nonspecific electrostatic attraction and specific hydrogen bonding and hydrophobic interactions. In the absence of bicarbonate, the anion binding site is occupied by a chloride ion or nitrate, an inhibitor directly competing with bicarbonate. These results provide a solid structural basis for the bicarbonate dependence of the enzymatic activity of type I DHNA-CoA synthases. The unique location of the bicarbonate ion in relation to the expected position of the substrate α-proton in the enzyme's active site suggests a critical catalytic role for the anionic cofactor as a catalytic base in enolate formation.

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Organizational Affiliation: 

Department of Chemistry and State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-Dihydroxy-2-naphthoyl-CoA synthase	A, B, C, D, E, F	285	Escherichia coli K-12	Mutation(s): 0  Gene Names: menB, b2262, JW2257 EC: 4.1.3.36
UniProt
Find proteins for P0ABU0 (Escherichia coli (strain K12)) Explore P0ABU0  Go to UniProtKB:  P0ABU0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	AA [auth F]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], O [auth B], Q [auth C], Z [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	BA [auth F], I [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT	G [auth A], L [auth B], M [auth B], P [auth C], T [auth D], U [auth D], W [auth E], X [auth E], Y [auth F]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
CL	J [auth A], N [auth B], R [auth C], S [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.222 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.367	α = 90
b = 133.888	β = 90
c = 153.25	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-11 
• Released Date: 2012-06-06 
Deposition Author(s): Sun, Y.R., Song, H.G., Li, J., Jiang, M., Li, Y., Zhou, J.H., Guo, Z.H.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2013-07-03
  Changes: Database references