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), 0.248 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 59.17 kDa 
  • Atom Count: 3,858 
  • Modeled Residue Count: 469 
  • Deposited Residue Count: 498 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [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), 0.248 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.219 (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

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Ligand Structure Quality Assessment 


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