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 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 2.0 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: https://doi.org/10.1021/acs.biochem.6b00889
  • Primary Citation of Related Structures:  
    5GTD

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-succinylbenzoate--CoA ligase
A, B
494Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: menEBSU30790
EC: 6.2.1.26
UniProt
Find proteins for P23971 (Bacillus subtilis (strain 168))
Explore P23971 
Go to UniProtKB:  P23971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23971
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
OSB
Query on OSB

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B]
2-SUCCINYLBENZOATE
C11 H10 O5
YIVWQNVQRXFZJB-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
IMD
Query on IMD

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K [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
CL
Query on CL

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C [auth A],
D [auth A],
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.814α = 90
b = 121.814β = 90
c = 98.563γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-04
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2024-05-29
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary