Ternary complex structure of a double mutant I454RA456K of o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis bound with AMP and its product analogue OSB-NCoA at 1.76 angstrom

Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-succinylbenzoate--CoA ligase
A, B, C, D
485Bacillus subtilis subsp. subtilis str. 168Mutation(s): 2 
Gene Names: menEBSU30790
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
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on S0N

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E [auth A],
IB [auth D],
RA [auth C],
W [auth B]
o-succinylbenzoyl-N-coenzyme A
C32 H45 N8 O20 P3
Query on AMP

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F [auth A],
SA [auth C]
C10 H14 N5 O7 P
Query on PEG

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BC [auth D]
FB [auth C]
GB [auth C]
OA [auth B]
PA [auth B]
BC [auth D],
FB [auth C],
GB [auth C],
OA [auth B],
PA [auth B],
T [auth A],
U [auth A]
C4 H10 O3
Query on CA

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HB [auth C],
QA [auth B],
V [auth A]
Query on MG

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AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JB [auth D],
K [auth A],
KB [auth D],
L [auth A],
LB [auth D],
M [auth A],
MB [auth D],
N [auth A],
NB [auth D],
OB [auth D],
PB [auth D],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C],
X [auth B],
Y [auth B],
Z [auth B]
Query on NA

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AB [auth C]
AC [auth D]
BB [auth C]
CB [auth C]
DB [auth C]
AB [auth C],
AC [auth D],
BB [auth C],
CB [auth C],
DB [auth C],
EB [auth C],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
O [auth A],
P [auth A],
Q [auth A],
QB [auth D],
R [auth A],
RB [auth D],
S [auth A],
SB [auth D],
TB [auth D],
UB [auth D],
VB [auth D],
WB [auth D],
XA [auth C],
XB [auth D],
YA [auth C],
YB [auth D],
ZA [auth C],
ZB [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.76 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.87α = 80.44
b = 96.36β = 77.96
c = 98.07γ = 81.11
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
Aimlessdata reduction

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: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description