PXD033471-1

PXD033471 is an original dataset announced via ProteomeXchange.

Title	Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13
Description	Mycobacterium polyketide synthase 13 (Pks13) is a protein complex comprised of a closely symmetric parallel dimer of chains, each encoding several enzymatic and transport functions. This module carries out the condensation of two different very long chain fatty acids to produce mycolic acids that are essential components of the mycobacterial cell wall. Here, we use cryo-EM, XL-MS, and integrative modeling to determine the structure and domain trajectories of the dimeric multi-enzyme Pks13 purified endogenously from mycobacteria under normal growth conditions. Structures of the multi-domain assembly revealed by cryogenic electron microscopy (cryoEM) define the ketosynthase (KS), linker, and acyltransferase (AT) domains, each at atomic resolution (1.8Å), with bound substrates defined at 2.4Å and 2.9Å resolution. Image classification reveals two distinct structures with alternate locations of the N-terminal acyl carrier protein (termed ACP1a, ACP1b) seen at 3.6Å and 4.6Å resolution respectively. These two structures suggest plausible intermediate states, related by a ~60Å movement of ACP1, on the pathway for substrate delivery from the fatty acyl-ACP ligase (FadD32) to the ketosynthase domain. The linking sequence between ACP1 and the KS includes an 11 amino acid sequence with 6 negatively charged side chains that lies in different positively charged grooves on the KS in ACP1a versus ACP1b structures. This charge complementarity between the extended chain and the grooves suggests some stabilization of these two distinct orientations. Other domains are visible at lower resolution and indicate flexibility relative to the KS-AT core. The chemical structures of three bound endogenous long chain fatty acid substrates with their proximal regions defined in the structures were determined by electrospray ionization mass spectrometry. The domain proximities were probed by chemical cross-linking and identified by mass spectrometry (XL-MS). These were incorporated into integrative structure modeling to define multiple domain configurations that transport the very long fatty acid chains throughout the multistep Pks13 mediated synthetic pathway.
HostingRepository	PRIDE
AnnounceDate	2023-06-13
AnnouncementXML	Submission_2023-06-13_10:20:13.555.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	RobynKaake
SpeciesList	scientific name: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155); NCBI TaxID: 246196;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-27 13:39:28	ID requested
⏵ 1	2023-06-13 10:20:14	announced
2	2023-11-14 09:00:52	announced	2023-11-14: Updated project metadata.

Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM, Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol, 30(3):296-308(2023) [pubmed]

submitter keyword: XL-MS, DSSO, polyketide synthase pks13, mycobacterium

Robyn MidoriKaake
contact affiliation	Department of Cellular and Molecular Pharmacology, School of Medicine, University of California San Francisco, USA
contact email	robyn.kaake@gladstone.ucsf.edu
lab head
RobynKaake
contact affiliation	Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
contact email	robyn.kaake@gladstone.ucsf.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033471
     1. Label: PRIDE project
     2. Name: Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13