8RZ6 | pdb_00008rz6

SeMet derivative structure of the condensation domain TomBC from the Tomaymycin non-ribosomal peptide synthetase

PDB DOI: https://doi.org/10.2210/pdb8RZ6/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Streptomyces regensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-12 Released: 2024-06-26
Deposition Author(s): Karanth, M., Schmelz, S., Kirkpatrick, J., Krausze, J., Scrima, A., Carlomagno, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.216 (Depositor), 0.199 (DCC)
R-Value Work:
0.172 (Depositor)
R-Value Observed:
0.175 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain.

Karanth, M.N., Kirkpatrick, J.P., Krausze, J., Schmelz, S., Scrima, A., Carlomagno, T.

(2024) Sci Adv 10: eadm9404-eadm9404

PubMed: 38896613 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adm9404
Primary Citation Related Structures:
8QNF, 8QPY, 8QRX, 8QSX, 8RZ6, 9A82, 9A83

PubMed Abstract:
In the quest for new bioactive substances, nonribosomal peptide synthetases (NRPS) provide biodiversity by synthesizing nonproteinaceous peptides with high cellular activity. NRPS machinery consists of multiple modules, each catalyzing a unique series of chemical reactions. Incomplete understanding of the biophysical principles orchestrating these reaction arrays limits the exploitation of NRPSs in synthetic biology. Here, we use nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to solve the conundrum of how intermodular recognition is coupled with loaded carrier protein specificity in the tomaymycin NRPS. We discover an adaptor domain that directly recruits the loaded carrier protein from the initiation module to the elongation module and reveal its mechanism of action. The adaptor domain of the type found here has specificity rules that could potentially be exploited in the design of engineered NRPS machinery.

Organizational Affiliation

Laboratory of Integrative Structural Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.

Macromolecule Content

Total Structure Weight: 120.04 kDa
Atom Count: 7,521
Modeled Residue Count: 881
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tomaymycin non-ribosomal peptide synthetase	A, B	537	Streptomyces regensis	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], I [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]