5MY0

KS-MAT DI-DOMAIN OF MOUSE FAS WITH MALONYL-COA

PDB DOI: https://doi.org/10.2210/pdb5MY0/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2017-01-25 Released: 2018-01-24
Deposition Author(s): Paithankar, K.S., Rittner, A., Huu, K.V., Grininger, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.222
R-Value Work: 0.188
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Characterization of the Polyspecific Transferase of Murine Type I Fatty Acid Synthase (FAS) and Implications for Polyketide Synthase (PKS) Engineering.

Rittner, A., Paithankar, K.S., Huu, K.V., Grininger, M.

(2018) ACS Chem Biol 13: 723-732

PubMed: 29328619 Search on PubMed
DOI: https://doi.org/10.1021/acschembio.7b00718
Primary Citation of Related Structures:
5MY0

PubMed Abstract:
Fatty acid synthases (FASs) and polyketide synthases (PKSs) condense acyl compounds to fatty acids and polyketides, respectively. Both, FASs and PKSs, harbor acyltransferases (ATs), which select substrates for condensation by β-ketoacyl synthases (KSs). Here, we present the structural and functional characterization of the polyspecific malonyl/acetyltransferase (MAT) of murine FAS. We assign kinetic constants for the transacylation of the native substrates, acetyl- and malonyl-CoA, and demonstrate the promiscuity of FAS to accept structurally and chemically diverse CoA-esters. X-ray structural data of the KS-MAT didomain in a malonyl-loaded state suggests a MAT-specific role of an active site arginine in transacylation. Owing to its enzymatic properties and its accessibility as a separate domain, MAT of murine FAS may serve as versatile tool for engineering PKSs to provide custom-tailored access to new polyketides that can be applied in antibiotic and antineoplastic therapy.

Organizational Affiliation

Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes , Goethe University Frankfurt , Max-von-Laue-Str. 15 , 60438 Frankfurt am Main , Germany.

Macromolecule Content

Total Structure Weight: 371.3 kDa
Atom Count: 25,992
Modelled Residue Count: 3,400
Deposited Residue Count: 3,408
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	A, D	852	Mus musculus	Mutation(s): 0 Gene Names: Fasn EC: 2.3.1.85 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 2.3.1.41 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt
Find proteins for P19096 (Mus musculus) Explore P19096 Go to UniProtKB: P19096
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19096
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	B, C	852	Mus musculus	Mutation(s): 0 Gene Names: Fasn EC: 2.3.1.85 (PDB Primary Data), 2.3.1.38 (PDB Primary Data), 2.3.1.39 (PDB Primary Data), 2.3.1.41 (PDB Primary Data), 1.1.1.100 (PDB Primary Data), 4.2.1.59 (PDB Primary Data), 1.3.1.39 (PDB Primary Data), 3.1.2.14 (PDB Primary Data)
UniProt
Find proteins for P19096 (Mus musculus) Explore P19096 Go to UniProtKB: P19096
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19096
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLC Query on MLC Download Ideal Coordinates CCD File SDF format, chain F [auth C] MOL2 format, chain F [auth C]	F [auth C]	MALONYL-COENZYME A C₂₄ H₃₈ N₇ O₁₉ P₃ S LTYOQGRJFJAKNA-DVVLENMVSA-N		Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth D]	E [auth A], G [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
K5L Query on K5L	A, D	L-PEPTIDE LINKING	C₆ H₉ N O₆		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.222
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.5281/zenodo.1136532

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.044	α = 90
b = 354.39	β = 90
c = 217.463	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
MOLREP	phasing
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-01-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-01-24
Type: Initial release
Version 1.1: 2018-03-28
Changes: Database references
Version 1.2: 2018-08-08
Changes: Data collection, Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Refinement description