8X8J | pdb_00008x8j

The structure of AbBioc in complex with inhibitor sinefungin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.250 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SFGClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

A bacterial methyltransferase that initiates biotin synthesis, an attractive anti-ESKAPE druggable pathway.

Su, Z.Zhang, W.Shi, Y.Cui, T.Xu, Y.Yang, R.Huang, M.Zhou, C.Zhang, H.Lu, T.Qu, J.He, Z.G.Gan, J.Feng, Y.

(2024) Sci Adv 10: eadp3954-eadp3954

  • DOI: https://doi.org/10.1126/sciadv.adp3954
  • Primary Citation of Related Structures:  
    8X8I, 8X8J

  • PubMed Abstract: 

    The covalently attached cofactor biotin plays pivotal roles in central metabolism. The top-priority ESKAPE-type pathogens, Acinetobacter baumannii and Klebsiella pneumoniae , constitute a public health challenge of global concern. Despite the fact that the late step of biotin synthesis is a validated anti-ESKAPE drug target, the primary stage remains fragmentarily understood. We report the functional definition of two BioC isoenzymes (AbBioC for A. baumannii and KpBioC for K. pneumoniae ) that act as malonyl-ACP methyltransferase and initiate biotin synthesis. The physiological requirement of biotin is diverse within ESKAPE pathogens. CRISPR-Cas9-based inactivation of bioC rendered A. baumannii and K. pneumoniae biotin auxotrophic. The availability of soluble AbBioC enabled the in vitro reconstitution of DTB/biotin synthesis. We solved two crystal structures of AbBioC bound to SAM cofactor (2.54 angstroms) and sinefungin (SIN) inhibitor (1.72 angstroms). Structural and functional study provided molecular basis for SIN inhibition of BioC. We demonstrated that BioC methyltransferase plays dual roles in K. pneumoniae infection and A. baumannii colistin resistance.


  • Organizational Affiliation

    Key Laboratory of Multiple Organ Failure (Ministry of Education), and Departments of Microbiology and General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Malonyl-[acyl-carrier protein] O-methyltransferase
A, B
249Acinetobacter baumanniiMutation(s): 0 
Gene Names: bioC
EC: 2.1.1.197
UniProt
Find proteins for A0A1E3M3A7 (Acinetobacter baumannii)
Explore A0A1E3M3A7 
Go to UniProtKB:  A0A1E3M3A7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1E3M3A7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SFG (Subject of Investigation/LOI)
Query on SFG

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
SINEFUNGIN
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO
Query on DIO

Download Ideal Coordinates CCD File 
H [auth A]1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.250 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.699α = 90
b = 56.547β = 101.13
c = 70.68γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SFGClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Key Reserch & Development Program of ChinaChina2023YFC2307100

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Database references