6RXR

Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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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

  • DOI: 10.1002/anie.202002899
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Stephanstrasse 7, 64295, Darmstadt, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacylaseA, B, C, D254Escherichia coli K-12Mutation(s): 3 
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
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UniProt GroupP75960
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4E, F, G, H11Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02309 
Go to UniProtKB:  P02309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KMQ
Query on KMQ
Download Ideal Coordinates CCD File 
I [auth E],
J [auth F],
K [auth G],
L [auth H]		[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
C19 H29 N5 O14 P2
JOKNWQJJLFYBKK-YVAUJSGTSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.38α = 90
b = 94.07β = 90.03
c = 94.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyNE1589/5-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references