4FIN | pdb_00004fin

Crystal Structure of EttA (formerly YjjK) - an E. coli ABC-type ATPase

• PDB DOI: https://doi.org/10.2210/pdb4FIN/pdb

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


• Deposited: 2012-06-09 Released: 2013-07-03 
• Deposition Author(s): Smith, P., Yuan, Y., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

The ABC-F protein EttA gates ribosome entry into the translation elongation cycle.

Boel, G., Smith, P.C., Ning, W., Englander, M.T., Chen, B., Hashem, Y., Testa, A.J., Fischer, J.J., Wieden, H.J., Frank, J., Gonzalez, R.L., Hunt, J.F.

(2014) Nat Struct Mol Biol 21: 143-151

• PubMed: 24389466 
• DOI: https://doi.org/10.1038/nsmb.2740
• Primary Citation Related Structures: 
  4FIN


• PubMed Abstract: 
  

  ABC-F proteins have evaded functional characterization even though they compose one of the most widely distributed branches of the ATP-binding cassette (ABC) superfamily. Herein, we demonstrate that YjjK, the most prevalent eubacterial ABC-F protein, gates ribosome entry into the translation elongation cycle through a nucleotide-dependent interaction sensitive to ATP/ADP ratio. Accordingly, we rename this protein energy-dependent translational throttle A (EttA). We determined the crystal structure of Escherichia coli EttA and used it to design mutants for biochemical studies including enzymological assays of the initial steps of protein synthesis. These studies suggest that EttA may regulate protein synthesis in energy-depleted cells, which have a low ATP/ADP ratio. Consistently with this inference, EttA-deleted cells exhibit a severe fitness defect in long-term stationary phase. These studies demonstrate that an ABC-F protein regulates protein synthesis via a new mechanism sensitive to cellular energy status.

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Organizational Affiliation: 
• 1] Department of Biological Sciences, Columbia University, New York, New York, USA. [2] Northeast Structural Genomics Consortium, Columbia University, New York, New York, USA.
1] Department of Biological Sciences, Columbia University, New York, New York, USA. [2].
Department of Chemistry, Columbia University, New York, New York, USA.
1] Department of Chemistry, Columbia University, New York, New York, USA. [2] Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, Medical Center, New York, New York, USA. [3].
Department of Biological Sciences, Columbia University, New York, New York, USA.
1] Department of Biochemistry, Columbia University Medical Center, New York, New York, USA. [2] Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, USA.
1] Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada. [2].
Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
1] Department of Biological Sciences, Columbia University, New York, New York, USA. [2] Department of Biochemistry, Columbia University Medical Center, New York, New York, USA. [3] Howard Hughes Medical Institute, Columbia University Medical Center, New York, New York, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 128.22 kDa 
• Atom Count: 8,943 
• Modeled Residue Count: 1,065 
• Deposited Residue Count: 1,110 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EttA (YjjK) ABCF family protein	A, B	555	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4391, JW4354, yjjK EC: 3.6.1
UniProt
Find proteins for P0A9W3 (Escherichia coli (strain K12)) Explore P0A9W3  Go to UniProtKB:  P0A9W3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	H [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
PGE	I [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], K [auth A], L [auth A], M [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.363	α = 90
b = 233.474	β = 91.29
c = 54.089	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Smith, P., Yuan, Y., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Structure summary
• Version 1.2: 2014-01-08
  Changes: Database references
• Version 1.3: 2014-03-05
  Changes: Database references
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary