6RXJ | pdb_00006rxj

Crystal structure of CobB wt in complex with H4K16-Acetyl peptide

• PDB DOI: https://doi.org/10.2210/pdb6RXJ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-06-08 Released: 2020-04-15 
• Deposition Author(s): Spinck, M., Gasper, R., Neumann, H.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Evolved, Selective Erasers of Distinct Lysine Acylations.

Spinck, M., Neumann-Staubitz, P., Ecke, M., Gasper, R., Neumann, H.

(2020) Angew Chem Int Ed Engl 59: 11142-11149

• PubMed: 32187803 
• DOI: https://doi.org/10.1002/anie.202002899
• Primary Citation Related Structures: 
  6RXJ, 6RXK, 6RXL, 6RXM, 6RXO, 6RXP, 6RXQ, 6RXR, 6RXS


• PubMed Abstract: 
  

  Lysine acylations, a family of diverse protein modifications varying in acyl-group length, charge, and saturation, are linked to many important physiological processes. Only a small set of substrate-promiscuous lysine acetyltransferases and deacetylases (KDACs) install and remove this vast variety of modifications. Engineered KDACs that remove only one type of acylation would help to dissect the different contributions of distinct acylations. We developed a bacterial selection system for the directed evolution of KDACs and identified variants up to 400 times more selective for butyryl-lysine compared to crotonyl-lysine. Structural analyses revealed that the enzyme adopts different conformational states depending on the type of acylation of the bound peptide. We used the butyryl-selective KDAC variant to shift the cellular acylation spectrum towards increased lysine crotonylation. These new enzymes will help in dissecting the roles of different lysine acylations in cell physiology.

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Organizational Affiliation: 
• Department of Structural Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.
Crystallography and Biophysics Unit, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany.
Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.74 kDa 
• Atom Count: 4,090 
• Modeled Residue Count: 485 
• Deposited Residue Count: 528 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase	A, B	254	Escherichia coli K-12	Mutation(s): 0  Gene Names: cobB, ycfY, b1120, JW1106 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt
Find proteins for P75960 (Escherichia coli (strain K12)) Explore P75960  Go to UniProtKB:  P75960

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C, D	10	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309  Go to UniProtKB:  P02309

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	C, D	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.1	α = 90
b = 131.26	β = 90
c = 58.54	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-15 
Deposition Author(s): Spinck, M., Gasper, R., Neumann, H.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	NE1589/5-1

Revision History  

• Version 1.0: 2020-04-15
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-01-24
  Changes: Refinement description
• Version 2.2: 2024-10-23
  Changes: Structure summary