9Z38 | pdb_00009z38

Crystal Structure of CalO4 from Micromonospora echinospora


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 
    0.193 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.162 (DCC) 

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9Z38

This is version 1.1 of the entry. See complete history

Literature

Thioester Bond Formation Catalyzed by CalO4: A beta-Ketoacyl-ACP Synthase III-like Acyltransferase in Calicheamicin Biosynthesis.

Pang, F.Peng, Y.J.Thadkapally, S.Townsend, C.A.

(2026) ACS Chem Biol 

  • DOI: https://doi.org/10.1021/acschembio.6c00389
  • Primary Citation Related Structures: 
    9Z38

  • PubMed Abstract: 

    β-Ketoacyl-ACP synthase (KAS) III enzymes play central roles in fatty acid biosynthesis and the production of various natural products. While their canonical function involves catalyzing C-C bond formation between acetyl-CoA and malonyl acyl-carrier-proteins (ACPs), an increasing number of non-canonical activities have been reported among KAS III homologues, including C-O and C-N bond formation. Here, we describe a KAS III family enzyme, CalO4, that catalyzes C-S bond formation during the biosynthesis of the potent antitumor agent calicheamicin. We successfully reconstituted its transacylation activities, demonstrated C-S bond formation, and assessed its substrate selectivity. Furthermore, X-ray crystallography combined with molecular docking and mutational analysis identified key residues likely involved in substrate selection and catalysis. This work not only expands the functional diversity of the KAS III family but also provides a potential biocatalyst for hindered C-S bond formation and a target for engineering novel calicheamicin-like or other bioactive compounds.


  • Organizational Affiliation
    • Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland21218, United States.

Macromolecule Content 

  • Total Structure Weight: 77.54 kDa 
  • Atom Count: 5,473 
  • Modeled Residue Count: 684 
  • Deposited Residue Count: 716 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase-3A,
B [auth C]
358Micromonospora echinosporaMutation(s): 0 
Gene Names: GA0070606_5687
UniProt
Find proteins for A0A1C6VYG5 (Micromonospora citrea)
Explore A0A1C6VYG5 
Go to UniProtKB:  A0A1C6VYG5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C6VYG5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
Q [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
N [auth C]
O [auth C]
G [auth A],
H [auth A],
I [auth A],
N [auth C],
O [auth C],
P [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
K [auth C]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth C],
L [auth C],
M [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free:  0.193 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.162 (DCC) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.696α = 90
b = 95.635β = 95.63
c = 172.584γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES001670

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-05
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Database references