6ULY

Adenylation domain of a keto acid-selecting NRPS module bound to keto acyl adenylate space group P212121

PDB DOI: https://doi.org/10.2210/pdb6ULY/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Bacillus stratosphericus LAMA 585
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-10-08 Released: 2020-02-19
Deposition Author(s): Alonzo, D.A., Chiche-Lapierre, C., Schmeing, T.M.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247
R-Value Work: 0.228
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural basis of keto acid utilization in nonribosomal depsipeptide synthesis.

Alonzo, D.A., Chiche-Lapierre, C., Tarry, M.J., Wang, J., Schmeing, T.M.

(2020) Nat Chem Biol 16: 493-496

PubMed: 32066969 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41589-020-0481-5
Primary Citation of Related Structures:
6ULW, 6ULX, 6ULY, 6ULZ

PubMed Abstract:
Nonribosomal depsipeptides are natural products composed of amino and hydroxy acid residues. The hydroxy acid residues often derive from α-keto acids, reduced by ketoreductase domains in the depsipeptide synthetases. Biochemistry and structures reveal the mechanism of discrimination for α-keto acids and a remarkable architecture: flanking intact adenylation and ketoreductase domains are sequences separated by >1,100 residues that form a split 'pseudoA _sub' domain, structurally important for the depsipeptide module's synthetic cycle.

Organizational Affiliation

Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montreal, Quebec, Canada.

Macromolecule Content

Total Structure Weight: 130.9 kDa
Atom Count: 8,676
Modelled Residue Count: 1,076
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid adenylation domain-containing protein	A, B	576	Bacillus stratosphericus LAMA 585	Mutation(s): 0 Gene Names: C883_1060
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QA7 (Subject of Investigation/LOI) Query on QA7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain R [auth B] MOL2 format, chain C [auth A] MOL2 format, chain R [auth B]	C [auth A], R [auth B]	5'-O-{(S)-hydroxy[(4-methyl-2-oxopentanoyl)oxy]phosphoryl}adenosine C₁₆ H₂₂ N₅ O₉ P QRKXCZFTEMACEI-SDBHATRESA-N		Interactions Focus chain C [auth A] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain R [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth A] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B]	Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]