5X8G

Binary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with its product analogue OSB-NCoA at 1.90 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the thioesterification conformation of Bacillus subtilis o-succinylbenzoyl-CoA synthetase reveals a distinct substrate-binding mode

Chen, Y.Li, T.L.Lin, X.Li, X.Li, X.D.Guo, Z.

(2017) J Biol Chem 292: 12296-12310

  • DOI: https://doi.org/10.1074/jbc.M117.790410
  • Primary Citation of Related Structures:  
    5X8F, 5X8G

  • PubMed Abstract: 

    o -Succinylbenzoyl-CoA (OSB-CoA) synthetase (MenE) is an essential enzyme in bacterial vitamin K biosynthesis and an important target in the development of new antibiotics. It is a member of the adenylating enzymes (ANL) family, which reconfigure their active site in two different active conformations, one for the adenylation half-reaction and the other for a thioesterification half-reaction, in a domain-alternation catalytic mechanism. Although several aspects of the adenylating mechanism in MenE have recently been uncovered, its thioesterification conformation remains elusive. Here, using a catalytically competent Bacillus subtilis mutant protein complexed with an OSB-CoA analogue, we determined MenE high-resolution structures to 1.76 and 1.90 Å resolution in a thioester-forming conformation. By comparison with the adenylation conformation, we found that MenE's C-domain rotates around the Ser-384 hinge by 139.5° during domain-alternation catalysis. The structures also revealed a thioesterification active site specifically conserved among MenE orthologues and a substrate-binding mode distinct from those of many other acyl/aryl-CoA synthetases. Of note, using site-directed mutagenesis, we identified several residues that specifically contribute to the thioesterification half-reaction without affecting the adenylation half-reaction. Moreover, we observed a substantial movement of the activated succinyl group in the thioesterification half-reaction. These findings provide new insights into the domain-alternation catalysis of a bacterial enzyme essential for vitamin K biosynthesis and of its adenylating homologues in the ANL enzyme family.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-succinylbenzoate--CoA ligaseA,
B,
C [auth D],
D [auth C]
485Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S0N
Query on S0N

Download Ideal Coordinates CCD File 
E [auth A],
JA [auth C],
O [auth B],
V [auth D]
o-succinylbenzoyl-N-coenzyme A
C32 H45 N8 O20 P3
QCTNXUGGWNSKFY-HSJNEKGZSA-N
PEG
Query on PEG

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AA [auth D]
BA [auth D]
HA [auth C]
IA [auth C]
L [auth A]
AA [auth D],
BA [auth D],
HA [auth C],
IA [auth C],
L [auth A],
M [auth A],
N [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CA
Query on CA

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CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
I [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
I [auth A],
J [auth A],
S [auth B],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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F [auth A]
G [auth A]
H [auth A]
KA [auth C]
P [auth B]
F [auth A],
G [auth A],
H [auth A],
KA [auth C],
P [auth B],
Q [auth B],
R [auth B],
W [auth D],
X [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
GA [auth C],
K [auth A],
T [auth B],
U [auth B],
Z [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.95α = 80.14
b = 96.48β = 77.81
c = 97.66γ = 81.17
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
Aimlessdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-08-09
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection, Derived calculations
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description