8PRV | pdb_00008prv

Asymmetric unit of the yeast fatty acid synthase in the non-rotated state with ACP at the ketosreductase domain (FASamn sample)

PDB DOI: https://doi.org/10.2210/pdb8PRV/pdb
EM Map EMD-17839: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2023-07-12 Released: 2023-11-22
Deposition Author(s): Singh, K., Bunzel, G., Graf, B., Yip, K.M., Stark, H., Chari, A.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Reconstruction of a fatty acid synthesis cycle from acyl carrier protein and cofactor structural snapshots.

Singh, K., Bunzel, G., Graf, B., Yip, K.M., Neumann-Schaal, M., Stark, H., Chari, A.

(2023) Cell 186: 5054-5067.e16

PubMed: 37949058 Search on PubMed
DOI: https://doi.org/10.1016/j.cell.2023.10.009
Primary Citation Related Structures:
8PRV, 8PRW, 8PS1, 8PS2, 8PS8, 8PS9, 8PSA, 8PSF, 8PSG, 8PSJ, 8PSK, 8PSL, 8PSM, 8PSP

PubMed Abstract:
Fatty acids (FAs) play a central metabolic role in living cells as constituents of membranes, cellular energy reserves, and second messenger precursors. A 2.6 MDa FA synthase (FAS), where the enzymatic reactions and structures are known, is responsible for FA biosynthesis in yeast. Essential in the yeast FAS catalytic cycle is the acyl carrier protein (ACP) that actively shuttles substrates, biosynthetic intermediates, and products from one active site to another. We resolve the S. cerevisiae FAS structure at 1.9 Å, elucidating cofactors and water networks involved in their recognition. Structural snapshots of ACP domains bound to various enzymatic domains allow the reconstruction of a full yeast FA biosynthesis cycle. The structural information suggests that each FAS functional unit could accommodate exogenous proteins to incorporate various enzymatic activities, and we show proof-of-concept experiments where ectopic proteins are used to modulate FAS product profiles.

Organizational Affiliation

Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 646.55 kDa
Atom Count: 29,814
Modeled Residue Count: 3,781
Deposited Residue Count: 5,825
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit alpha	A, B	1,887	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.3.1.86 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 2.3.1.41 (PDB Primary Data)
UniProt
Find proteins for P19097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19097 Go to UniProtKB: P19097
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19097
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit beta	C [auth G]	2,051	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.3.1.86 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.9 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt
Find proteins for P07149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07149 Go to UniProtKB: P07149
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07149
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA (Subject of Investigation/LOI) Query on COA Download:Ideal Coordinates CCD File SDF format, chain H [auth G] MOL2 format, chain H [auth G] mmCIF format, chain H [auth G]	H [auth G]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain H [auth G] Interactions & Density Focus chain H [auth G]
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain G SDF format, chain D [auth A] MOL2 format, chain G MOL2 format, chain D [auth A] mmCIF format, chain G mmCIF format, chain D [auth A]	D [auth A], G	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain G Interactions & Density Focus chain D [auth A] Focus chain G
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain F [auth G] MOL2 format, chain F [auth G] mmCIF format, chain F [auth G]	F [auth G]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain F [auth G] Interactions & Density Focus chain F [auth G]
A5S (Subject of Investigation/LOI) Query on A5S Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylidenebutanethioate C₁₅ H₂₇ N₂ O₉ P S YNABGOTVLHSZGL-ZDUSSCGKSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]