6HXA

AntI from P. luminescens catalyses terminal polyketide shortening in the biosynthesis of anthraquinones

PDB DOI: https://doi.org/10.2210/pdb6HXA/pdb

Classification: LYASE
Organism(s): Photorhabdus luminescens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-16 Released: 2019-08-07
Deposition Author(s): Zhou, Q., Braeuer, A., Grammbitter, G., Schmalhofer, M., Saura, P., Adihou, H., Kaila, V.R.I., Groll, M., Bode, H.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.204
R-Value Work: 0.168
R-Value Observed: 0.170

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Molecular mechanism of polyketide shortening in anthraquinone biosynthesis ofPhotorhabdus luminescens.

Zhou, Q., Brauer, A., Adihou, H., Schmalhofer, M., Saura, P., Grammbitter, G.L.C., Kaila, V.R.I., Groll, M., Bode, H.B.

(2019) Chem Sci 10: 6341-6349

PubMed: 31341589 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/c9sc00749k
Primary Citation of Related Structures:
6HXA

PubMed Abstract:
Anthraquinones, a widely distributed class of aromatic natural products, are produced by a type II polyketide synthase system in the Gram-negative bacterium Photorhabdus luminescens . Heterologous expression of the antABCDEFGHI anthraquinone biosynthetic gene cluster in Escherichia coli identified AntI as an unusual lyase, catalysing terminal polyketide shortening prior to formation of the third aromatic ring. Functional in vitro and in vivo analysis of AntI using X-ray crystallography, structure-based mutagenesis, and molecular simulations revealed that AntI converts a defined octaketide to the tricyclic anthraquinone ring via retro-Claisen and Dieckmann reactions. Thus, AntI catalyses a so far unobserved multistep reaction in this PKS system.

Organizational Affiliation

Molekulare Biotechnologie , Fachbereich Biowissenschaften , Buchmann Institute for Molecular Life Sciences (BMLS) , Goethe Universität Frankfurt , Max-von-Laue-Str. 15, Max-von-Laue-Str. 9 , 60438 Frankfurt am Main , Germany . Email: [email protected].

Macromolecule Content

Total Structure Weight: 46.13 kDa
Atom Count: 3,253
Modelled Residue Count: 375
Deposited Residue Count: 399
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AntI	A	399	Photorhabdus luminescens	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MZT8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]