5GTD

o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis in Complex with the Acyl-adenylate Intermediate OSB-AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanistic Insights from the Crystal Structure of Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase Complexed with the Adenylate Intermediate

Chen, Y.Jiang, Y.Guo, Z.

(2016) Biochemistry 55: 6685-6695

  • DOI: 10.1021/acs.biochem.6b00889

  • PubMed Abstract: 
  • o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and p ...

    o-Succinylbenzoyl-CoA (OSB-CoA) synthetase, or MenE, catalyzes an essential step in vitamin K biosynthesis and is a valuable drug target. Like many other adenylating enzymes, it changes its structure to accommodate substrate binding, catalysis, and product release along the path of a domain alternation catalytic mechanism. We have determined the crystal structure of its complex with the adenylation product, o-succinylbenzoyl-adenosine monophosphate (OSB-AMP), and captured a new postadenylation state. This structure presents unique features such as a strained conformation for the bound adenylate intermediate to indicate that it represents the enzyme state after completion of the adenylation reaction but before release of the C domain in its transition to the thioesterification conformation. By comparison to the ATP-bound preadenylation conformation, structural changes are identified in both the reactants and the active site to allow inference about how these changes accommodate and facilitate the adenylation reaction and to directly support an in-line backside attack nucleophilic substitution mechanism for the first half-reaction. Mutational analysis suggests that the conserved His196 plays an important role in desolvation of the active site rather than stabilizing the transition state of the adenylation reaction. In addition, comparison of the new structure with a previously determined OSB-AMP-bound structure of the same enzyme allows us to propose a release mechanism of the C domain in its alteration to form the thioesterification conformation. These findings allow us to better understand the domain alternation catalytic mechanism of MenE as well as many other adenylating enzymes.


    Related Citations: 
    • Structural Basis for the ATP-dependent Configuration of Adenylation Active Site in Bacillus subtilis o-Succinylbenzoyl-CoA Synthetase.
      Chen, Y.,Sun, Y.,Song, H.,Guo, Z.
      (2015) J.BIOL.CHEM. --: --


    Organizational Affiliation

    Department of Chemistry, The Hong Kong University of Science and Technology , Clear Water Bay, Kowloon, Hong Kong SAR, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-succinylbenzoate--CoA ligase
A, B
494Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: menE
EC: 6.2.1.26
Find proteins for P23971 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P23971
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
A
Query on A

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Download CCD File 
A, B
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
OSB
Query on OSB

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Download CCD File 
A, B
2-SUCCINYLBENZOATE
O-SUCCINYLBENZOATE
C11 H10 O5
YIVWQNVQRXFZJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 121.814α = 90.00
b = 121.814β = 90.00
c = 98.563γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-20 
  • Released Date: 2017-01-04 
  • Deposition Author(s): Chen, Y., Guo, Z.

Funding OrganizationLocationGrant Number
the University Grants Council of the Government of the Hong Kong Special Administrative RegionHong KongSBI14SC05

Revision History 

  • Version 1.0: 2017-01-04
    Type: Initial release