3HMJ

Saccharomyces cerevisiae FAS type I

PDB DOI: https://doi.org/10.2210/pdb3HMJ/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2009-05-29 Released: 2009-09-01
Deposition Author(s): Johansson, P., Mulinacci, B., Koestler, C., Vollrath, R., Oesterhelt, D., Grininger, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.267
R-Value Work: 0.266
R-Value Observed: 0.266

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Multimeric options for the auto-activation of the Saccharomyces cerevisiae FAS type I megasynthase

Johansson, P., Mulinacci, B., Koestler, C., Vollrath, R., Oesterhelt, D., Grininger, M.

(2009) Structure 17: 1063-1074

PubMed: 19679086 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2009.06.014
Primary Citation of Related Structures:
2WAS, 2WAT, 3HMJ

PubMed Abstract:
The fungal type I fatty acid synthase (FAS) is a 2.6 MDa multienzyme complex, catalyzing all necessary steps for the synthesis of long acyl chains. To be catalytically competent, the FAS must be activated by a posttranslational modification of the central acyl carrier domain (ACP) by an intrinsic phosphopantetheine transferase (PPT). However, recent X-ray structures of the fungal FAS revealed a barrel-shaped architecture, with PPT located at the outside of the barrel wall, spatially separated from the ACP caged in the inner volume. This separation indicated that the activation has to proceed before the assembly to the mature complex, in a conformation where the ACP and PPT domains can meet. To gain insight into the auto-activation reaction and also into the fungal FAS assembly pathway, we structurally and functionally characterized the Saccharomyces cerevisiae FAS type I PPT as part of the multienzyme protein and as an isolated domain.

Organizational Affiliation

Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany. [email protected]

Macromolecule Content

Total Structure Weight: 1,310.42 kDa
Atom Count: 88,830
Modelled Residue Count: 11,349
Deposited Residue Count: 11,814
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit alpha	A, B, C	1,887	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: FAS2 EC: 2.3.1.86 (PDB Primary Data), 2.3.1.41 (UniProt), 1.1.1.100 (UniProt)
UniProt
Find proteins for P19097 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P19097 Go to UniProtKB: P19097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19097
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fatty acid synthase subunit beta	D [auth G], E [auth H], F [auth I]	2,051	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: FAS1 EC: 2.3.1.86 (PDB Primary Data), 3.1.2.14 (UniProt), 2.3.1.38 (UniProt), 4.2.1.59 (UniProt), 2.3.1.39 (UniProt), 1.3.1.9 (UniProt)
UniProt
Find proteins for P07149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07149 Go to UniProtKB: P07149
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07149
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain K [auth H] SDF format, chain J [auth G] SDF format, chain L [auth I] MOL2 format, chain K [auth H] MOL2 format, chain J [auth G] MOL2 format, chain L [auth I] mmCIF format, chain K [auth H] mmCIF format, chain J [auth G] mmCIF format, chain L [auth I]	J [auth G], K [auth H], L [auth I]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I] Interactions & Density Focus chain J [auth G] Focus chain K [auth H] Focus chain L [auth I]
CER Query on CER Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C]	G [auth A], H [auth B], I [auth C]	(2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE C₁₂ H₁₉ N O₃ QEPYZBPOTYDXNA-FECJWDPASA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.267
R-Value Work: 0.266
R-Value Observed: 0.266
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.884	α = 90
b = 231.884	β = 90
c = 756.784	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
Coot	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description