5F38

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


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 

Starting Model: experimental
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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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferaseA [auth B]393Escherichia coli K-12Mutation(s): 0 
Gene Names: atoBb2224JW2218
EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12))
Explore P76461 
Go to UniProtKB:  P76461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76461
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferaseB [auth A]394Escherichia coli K-12Mutation(s): 0 
Gene Names: atoBb2224JW2218
EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12))
Explore P76461 
Go to UniProtKB:  P76461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76461
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferaseC [auth D]394Escherichia coli K-12Mutation(s): 0 
Gene Names: atoBb2224JW2218
EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12))
Explore P76461 
Go to UniProtKB:  P76461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76461
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferaseD [auth C]395Escherichia coli K-12Mutation(s): 0 
Gene Names: atoBb2224JW2218
EC: 2.3.1.9
UniProt
Find proteins for P76461 (Escherichia coli (strain K12))
Explore P76461 
Go to UniProtKB:  P76461
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76461
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COZ
Query on COZ

Download Ideal Coordinates CCD File 
E [auth B]COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-HDCXRZRFSA-N
5UG
Query on 5UG

Download Ideal Coordinates CCD File 
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
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
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
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A [auth B]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
MLY
Query on MLY
A [auth B]L-PEPTIDE LINKINGC8 H18 N2 O2LYS
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 = 73.794α = 90
b = 76.254β = 90
c = 266.607γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DBTIndiaBT/IN/FINNISH/27/MRNM/2009

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description