5F38

X-ray crystal structure of a thiolase from Escherichia coli at 1.8 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb5F38/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-02 Released: 2016-07-13 
• Deposition Author(s): Ithayaraja, M., Neelanjana, J., Wierenga, R., Savithri, H.S., Murthy, M.R.N.
• Funding Organization(s): DBT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Crystal structure of a thiolase from Escherichia coli at 1.8 angstrom resolution.

Ithayaraja, M., Janardan, N., Wierenga, R.K., Savithri, H.S., Murthy, M.R.

(2016) Acta Crystallogr F Struct Biol Commun 72: 534-544

• PubMed: 27380370 
• DOI: https://doi.org/10.1107/S2053230X16008451
• Primary Citation of Related Structures:  
  5F0V, 5F38


• PubMed Abstract: 
  

Thiolases catalyze the Claisen condensation of two acetyl-CoA molecules to give acetoacetyl-CoA, as well as the reverse degradative reaction. Four genes coding for thiolases or thiolase-like proteins are found in the Escherichia coli genome. In this communication, the successful cloning, purification, crystallization and structure determination at 1.8 Å resolution of a homotetrameric E. coli thiolase are reported. The structure of E. coli thiolase co-crystallized with acetyl-CoA at 1.9 Å resolution is also reported. As observed in other tetrameric thiolases, the present E. coli thiolase is a dimer of two tight dimers and probably functions as a biodegradative enzyme. Comparison of the structure and biochemical properties of the E. coli enzyme with those of other well studied thiolases reveals certain novel features of this enzyme, such as the modification of a lysine in the dimeric interface, the possible oxidation of the catalytic Cys88 in the structure of the enzyme obtained in the presence of CoA and active-site hydration. The tetrameric enzyme also displays an interesting departure from exact 222 symmetry, which is probably related to the deformation of the tetramerization domain that stabilizes the oligomeric structure of the protein. The current study allows the identification of substrate-binding amino-acid residues and water networks at the active site and provides the structural framework required for understanding the biochemical properties as well as the physiological function of this E. coli thiolase.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560 012, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 165.16 kDa 
• Atom Count: 12,020 
• Modelled Residue Count: 1,553 
• Deposited Residue Count: 1,576 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A [auth B]	393	Escherichia coli K-12	Mutation(s): 0  Gene Names: atoB, b2224, JW2218 EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12)) Explore P76461  Go to UniProtKB:  P76461

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	B [auth A]	394	Escherichia coli K-12	Mutation(s): 0  Gene Names: atoB, b2224, JW2218 EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12)) Explore P76461  Go to UniProtKB:  P76461

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	C [auth D]	394	Escherichia coli K-12	Mutation(s): 0  Gene Names: atoB, b2224, JW2218 EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12)) Explore P76461  Go to UniProtKB:  P76461

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	D [auth C]	395	Escherichia coli K-12	Mutation(s): 0  Gene Names: atoB, b2224, JW2218 EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12)) Explore P76461  Go to UniProtKB:  P76461

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COZ	E [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-HDCXRZRFSA-N
5UG	HA [auth C], W [auth D]	[(3~{S})-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-4-[[3-oxidanylidene-3-(2-sulfanylethylamino)propyl]amino]butyl] phosphono hydrogen phosphate C11 H24 N2 O10 P2 S UQURMDBHCKDEJS-SECBINFHSA-N
EDO	AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], F [auth B], FA [auth D], G [auth B], GA [auth D], H [auth B], I [auth B], IA [auth C], J [auth B], JA [auth C], K [auth B], KA [auth C], L [auth B], LA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], X [auth D], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A [auth B]	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MLY	A [auth B]	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.235 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.794	α = 90
b = 76.254	β = 90
c = 266.607	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Ithayaraja, M., Neelanjana, J., Wierenga, R., Savithri, H.S., Murthy, M.R.N.

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Funding Organization	Location	Grant Number
DBT	India	BT/IN/FINNISH/27/MRNM/2009

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references, Derived calculations