6B0U | pdb_00006b0u

Crystal structure of acetyltransferase Eis from Mycobacterium tuberculosis in complex with a Lys-containing peptide

• PDB DOI: https://doi.org/10.2210/pdb6B0U/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-15 Released: 2018-01-31 
• Deposition Author(s): Biswas, T., Pang, A.H., Garneau-Tsodikova, S., Tsodikov, O.V.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight.

Green, K.D., Biswas, T., Pang, A.H., Willby, M.J., Reed, M.S., Stuchlik, O., Pohl, J., Posey, J.E., Tsodikov, O.V., Garneau-Tsodikova, S.

(2018) Biochemistry 57: 781-790

• PubMed: 29345920 
• DOI: https://doi.org/10.1021/acs.biochem.7b01089
• Primary Citation Related Structures: 
  6B0U


• PubMed Abstract: 
  

  Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD ⁺ -dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.

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Organizational Affiliation: 
• Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States.
Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A6B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 145.69 kDa 
• Atom Count: 9,234 
• Modeled Residue Count: 1,183 
• Deposited Residue Count: 1,302 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyltransferase Eis	A, B, C	428	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: eis, Rv2416c, MTCY253.04 EC: 2.3.1
UniProt
Find proteins for P9WFK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFK7  Go to UniProtKB:  P9WFK7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide ATKAPAKKA	D, E	9	Mycobacterium tuberculosis H37Rv	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	F [auth A], G [auth A], H [auth B], I [auth C], J [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.902	α = 90
b = 175.866	β = 120.49
c = 85.129	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-2000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Biswas, T., Pang, A.H., Garneau-Tsodikova, S., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI090048

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary