6ULW | pdb_00006ulw

Adenylation, ketoreductase, and pseudo Asub multidomain structure of a keto acid-selecting NRPS module

PDB DOI: https://doi.org/10.2210/pdb6ULW/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., Wang, J., 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: 3.40 Å
R-Value Free:
0.275 (Depositor), 0.277 (DCC)
R-Value Work:
0.228 (Depositor), 0.233 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41589-020-0481-5
Primary Citation 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: 596.07 kDa
Atom Count: 37,840
Modeled Residue Count: 4,798
Deposited Residue Count: 5,308
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid adenylation domain-containing protein	A, B, C, D	1,327	Bacillus stratosphericus LAMA 585	Mutation(s): 0 Gene Names: C883_1060

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], L [auth D], M [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.275 (Depositor), 0.277 (DCC)
R-Value Work: 0.228 (Depositor), 0.233 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.66	α = 90
b = 143.66	β = 90
c = 431.87	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-02-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2020-02-19
Type: Initial release
Version 1.1: 2020-03-04
Changes: Database references
Version 1.2: 2020-05-06
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description