8K4R | pdb_00008k4r

Deposited: 2023-07-20 Released: 2023-11-01
Deposition Author(s): Miyanaga, A., Nagata, K., Nakajima, J., Chisuga, T., Kudo, F., Eguchi, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

(2023) ACS Chem Biol 18: 2343-2348

PubMed Abstract:
Adenylation enzymes activate amino acid substrates to aminoacyl adenylates and generally transfer this moiety onto the thiol group of the phosphopantetheine arm of a carrier protein for the selective incorporation of aminoacyl building blocks in natural product biosynthesis. In contrast to the canonical thioester-forming adenylation enzymes, the amide-forming adenylation enzyme VinM transfers an l-alanyl group onto the amino group of the aminoacyl unit attached to the phosphopantetheine arm of the carrier protein VinL to generate dipeptidyl-VinL in vicenistatin biosynthesis. It is unclear how VinM distinguishes aminoacyl-VinL from VinL for amide bond formation. Herein we describe structural and biochemical analyses of VinM. We determined the crystal structure of VinM in complex with VinL using a designed pantetheine-type cross-linking probe. The VinM-VinL complex structure in combination with site-directed mutagenesis analysis revealed that the interactions with both the phosphopantetheine arm and VinL are critical for the amide-forming activity of VinM.

Organizational Affiliation

Macromolecule Content

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-ribosomal peptide synthetase	A, C	540	Streptomyces halstedii	Mutation(s): 1 Gene Names: vinM
UniProt
Find proteins for Q76KY3 (Streptomyces halstedii) Explore Q76KY3 Go to UniProtKB: Q76KY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q76KY3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-carrier-protein	B, D	102	Streptomyces halstedii	Mutation(s): 0 Gene Names: vinL
UniProt
Find proteins for Q76KY4 (Streptomyces halstedii) Explore Q76KY4 Go to UniProtKB: Q76KY4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q76KY4
Sequence Annotations Expand
Reference Sequence

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VPI (Subject of Investigation/LOI) Query on VPI Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	F [auth B], H [auth D]	[(3~{R})-4-[[3-(6-acetamidohexylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate C₁₇ H₃₄ N₃ O₈ P KSMJRHVJQGTOAX-HNNXBMFYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain E [auth A]	E [auth A], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth C]