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: 199.90 kDa 
• Atom Count: 14295 
• Modelled Residue Count: 1686 
• Deposited Residue Count: 1734 
• Unique protein chains: 1

3T88

Crystal structure of Escherichia coli MenB in complex with substrate analogue, OSB-NCoA

• PDB DOI: 10.2210/pdb3T88/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-08-24 
• Deposition Author(s): Li, H.-J., Li, X., Liu, N., Zhang, H., Truglio, J., Mishra, S., Kisker, C., Garcia-Diaz, M., Tonge, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.195 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Literature

Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member.

Li, H.J., Li, X., Liu, N., Zhang, H., Truglio, J.J., Mishra, S., Kisker, C., Garcia-Diaz, M., Tonge, P.J.

(2011) Biochemistry 50: 9532-9544

• PubMed: 21830810 
• DOI: 10.1021/bi200877x
• Primary Citation of Related Structures:  
  3T88, 3T89, 3T8A, 3T8B


• PubMed Abstract: 
  

MenB, the 1,4-dihydroxy-2-naphthoyl-CoA synthase from the bacterial menaquinone biosynthesis pathway, catalyzes an intramolecular Claisen condensation (Dieckmann reaction) in which the electrophile is an unactivated carboxylic acid. Mechanistic studies on this crotonase family member have been hindered by partial active site disorder in existing MenB X-ray structures. In the current work the 2.0 Å structure of O-succinylbenzoyl-aminoCoA (OSB-NCoA) bound to the MenB from Escherichia coli provides important insight into the catalytic mechanism by revealing the position of all active site residues. This has been accomplished by the use of a stable analogue of the O-succinylbenzoyl-CoA (OSB-CoA) substrate in which the CoA thiol has been replaced by an amine. The resulting OSB-NCoA is stable, and the X-ray structure of this molecule bound to MenB reveals the structure of the enzyme-substrate complex poised for carbon-carbon bond formation. The structural data support a mechanism in which two conserved active site Tyr residues, Y97 and Y258, participate directly in the intramolecular transfer of the substrate α-proton to the benzylic carboxylate of the substrate, leading to protonation of the electrophile and formation of the required carbanion. Y97 and Y258 are also ideally positioned to function as the second oxyanion hole required for stabilization of the tetrahedral intermediate formed during carbon-carbon bond formation. In contrast, D163, which is structurally homologous to the acid-base catalyst E144 in crotonase (enoyl-CoA hydratase), is not directly involved in carbanion formation and may instead play a structural role by stabilizing the loop that carries Y97. When similar studies were performed on the MenB from Mycobacterium tuberculosis, a twisted hexamer was unexpectedly observed, demonstrating the flexibility of the interfacial loops that are involved in the generation of the novel tertiary and quaternary structures found in the crotonase superfamily. This work reinforces the utility of using a stable substrate analogue as a mechanistic probe in which only one atom has been altered leading to a decrease in α-proton acidity.

---

Organizational Affiliation: 

Institute for Chemical Biology & Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-Dihydroxy-2-naphthoyl-CoA synthase	A, B, C, D, E, F	289	Escherichia coli	Mutation(s): 0  Gene Names: b2262 EC: 4.1.3.36
UniProt
Find proteins for P0ABU0 (Escherichia coli (strain K12)) Explore P0ABU0  Go to UniProtKB:  P0ABU0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S0N	AA [auth F], G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]	o-succinylbenzoyl-N-coenzyme A C32 H45 N8 O20 P3 QCTNXUGGWNSKFY-HSJNEKGZSA-N
PGE	CA [auth F], I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	DA [auth F], J [auth A], N [auth B], R [auth C], V [auth D], Z [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	BA [auth F], H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.195 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.493	α = 90
b = 141.791	β = 90
c = 89.122	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-01 
• Released Date: 2011-08-24 
Deposition Author(s): Li, H.-J., Li, X., Liu, N., Zhang, H., Truglio, J., Mishra, S., Kisker, C., Garcia-Diaz, M., Tonge, P.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Structure summary