8QD6 | pdb_00008qd6

AntI Ser245DHA (PMSF)

• PDB DOI: https://doi.org/10.2210/pdb8QD6/pdb

• Classification: LYASE
• Organism(s): Photorhabdus laumondii subsp. laumondii TTO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-08-28 Released: 2024-03-13 
• Deposition Author(s): Schmalhofer, M., Vagstad, A.L., Zhou, Q., Bode, H.B., Groll, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.188 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: other

Literature

Polyketide Trimming Shapes Dihydroxynaphthalene-Melanin and Anthraquinone Pigments.

Schmalhofer, M., Vagstad, A.L., Zhou, Q., Bode, H.B., Groll, M.

(2024) Adv Sci (Weinh) 11: e2400184-e2400184

• PubMed: 38491909 
• DOI: https://doi.org/10.1002/advs.202400184
• Primary Citation Related Structures: 
  8QBH, 8QBI, 8QD1, 8QD2, 8QD3, 8QD4, 8QD5, 8QD6, 8QD7, 8QD8, 8QD9, 8QDA, 8QDB


• PubMed Abstract: 
  

  Pigments such as anthraquinones (AQs) and melanins are antioxidants, protectants, or virulence factors. AQs from the entomopathogenic bacterium Photorhabdus laumondii are produced by a modular type II polyketide synthase system. A key enzyme involved in AQ biosynthesis is PlAntI, which catalyzes the hydrolysis of the bicyclic-intermediate-loaded acyl carrier protein, polyketide trimming, and assembly of the aromatic AQ scaffold. Here, multiple crystal structures of PlAntI in various conformations and with bound substrate surrogates or inhibitors are reported. Structure-based mutagenesis and activity assays provide experimental insights into the three sequential reaction steps to yield the natural product AQ-256. For comparison, a series of ligand-complex structures of two functionally related hydrolases involved in the biosynthesis of 1,8-dihydroxynaphthalene-melanin in pathogenic fungi is determined. These data provide fundamental insights into the mechanism of polyketide trimming that shapes pigments in pro- and eukaryotes.

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Organizational Affiliation: 
• TUM School of Natural Sciences, Department of Bioscience, Centre for Protein Assemblies, Chair of Biochemistry, Technical University of Munich, 85748, Garching, Germany.
Eidgenössische Technische Hochschule (ETH) Zürich, Institute of Microbiology, Zürich, 8093, Switzerland.
Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt, Germany.
Department of Chemistry, Phillips Universität Marburg, 35043, Marburg, Germany.
Center for Synthetic Microbiology (SYNMIKRO), Phillips Universität Marburg, 35043, Marburg, Germany.
Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.28 kDa 
• Atom Count: 3,252 
• Modeled Residue Count: 377 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17	A	400	Photorhabdus laumondii subsp. laumondii TTO1	Mutation(s): 0  Gene Names: plu4186
UniProt
Find proteins for Q7MZT8 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)) Explore Q7MZT8  Go to UniProtKB:  Q7MZT8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.188 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.72	α = 90
b = 154.97	β = 90
c = 91.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Schmalhofer, M., Vagstad, A.L., Zhou, Q., Bode, H.B., Groll, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB 1309 - 325871075

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Database references