4U5Y | pdb_00004u5y

Crystal Structure of the complex between the GNAT domain of S. lividans PAT and the acetyl-CoA synthetase C-terminal domain of S. enterica

• PDB DOI: https://doi.org/10.2210/pdb4U5Y/pdb

• Classification: LIGASE
• Organism(s): Streptomyces lividans TK24, Salmonella enterica subsp. enterica serovar Paratyphi B str. ATCC 10719
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-07-25 Released: 2014-11-19 
• Deposition Author(s): Taylor, K.C., Tucker, A.C., Rank, K.C., Escalante-Semerena, J.C., Rayment, I.
• Funding Organization(s): USPHS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Models: experimental

Literature

Insights into the specificity of lysine acetyltransferases.

Tucker, A.C., Taylor, K.C., Rank, K.C., Rayment, I., Escalante-Semerena, J.C.

(2014) J Biological Chem 289: 36249-36262

• PubMed: 25381442 
• DOI: https://doi.org/10.1074/jbc.M114.613901
• Primary Citation Related Structures: 
  4NXY, 4U5Y


• PubMed Abstract: 
  

  Reversible lysine acetylation by protein acetyltransferases is a conserved regulatory mechanism that controls diverse cellular pathways. Gcn5-related N-acetyltransferases (GNATs), named after their founding member, are found in all domains of life. GNATs are known for their role as histone acetyltransferases, but non-histone bacterial protein acetytransferases have been identified. Only structures of GNAT complexes with short histone peptide substrates are available in databases. Given the biological importance of this modification and the abundance of lysine in polypeptides, how specificity is attained for larger protein substrates is central to understanding acetyl-lysine-regulated networks. Here we report the structure of a GNAT in complex with a globular protein substrate solved to 1.9 Å. GNAT binds the protein substrate with extensive surface interactions distinct from those reported for GNAT-peptide complexes. Our data reveal determinants needed for the recognition of a protein substrate and provide insight into the specificity of GNATs.

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Organizational Affiliation: 
• From the Department of Microbiology, University of Georgia, Athens, Georgia 30602 and.
the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706.
From the Department of Microbiology, University of Georgia, Athens, Georgia 30602 and [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 36.4 kDa 
• Atom Count: 2,396 
• Modeled Residue Count: 280 
• Deposited Residue Count: 329 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA synthetase	A	194	Streptomyces lividans TK24	Mutation(s): 1  Gene Names: SSPG_01886

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase	B [auth D]	135	Salmonella enterica subsp. enterica serovar Paratyphi B str. ATCC 10719	Mutation(s): 1  Gene Names: acs, SEEPB719_19728 EC: 6.2.1.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.478	α = 90
b = 66.524	β = 90
c = 138.539	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Taylor, K.C., Tucker, A.C., Rank, K.C., Escalante-Semerena, J.C., Rayment, I.

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Funding Organization	Location	Grant Number
USPHS	United States	GM062203
USPHS	United States	GM083987

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references
• Version 1.2: 2015-01-14
  Changes: Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy