6AG5

Crystal structure of Ard1 N-terminal acetyltransferase E88H/H127E mutant from Sulfolobus solfataricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Adaptation of thermophilic acetyltransferase to a water-mediated catalytic mechanism.

Chang, Y.Y.Hagawa, S.Hsu, C.H.

(2020) Chem Commun (Camb) 56: 10537-10540

  • DOI: 10.1039/d0cc04305b
  • Primary Citation of Related Structures:  
    6AG5, 6AG4

  • PubMed Abstract: 
  • The common mechanism of N-acetyltransferases (NATs) is a water-mediated catalysis, which is not conducive to thermophilic acetyltransferases. The crystal structure of SsArd1 shows an ordered catalytic water molecule in a trap formed by the residues H88 and E127 ...

    The common mechanism of N-acetyltransferases (NATs) is a water-mediated catalysis, which is not conducive to thermophilic acetyltransferases. The crystal structure of SsArd1 shows an ordered catalytic water molecule in a trap formed by the residues H88 and E127. Structure-guided mutagenesis, kinetic studies and MD simulation indicated that the turnover rates of H88A, E127A and H88A/E127A mutants were low, but that of the H88E/E127H mutant could be restored to the level of the wild type.


    Related Citations: 
    • Structural Basis for Substrate-specific Acetylation of Nalpha-acetyltransferase Ard1 from Sulfolobus solfataricus
      Chang, Y.Y., Hsu, C.H.
      (2015) Sci Rep 5: --

    Organizational Affiliation

    Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. andyhsu@ntu.edu.tw and Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-alpha-acetyltransferaseA175Saccharolobus solfataricus P2Mutation(s): 2 
Gene Names: AsArd1ard1SSO0209
EC: 2.3.1.255 (PDB Primary Data), 2.3.1.258 (PDB Primary Data)
UniProt
Find proteins for Q980R9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q980R9 
Go to UniProtKB:  Q980R9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO

Download Ideal Coordinates CCD File 
B [auth A]ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.217α = 90
b = 52.926β = 90
c = 73.576γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-08-09 
  • Released Date: 2019-08-14 
  • Deposition Author(s): Chang, Y.Y., Hsu, C.H.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan103-2113-M-002 -009 -MY2

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2020-09-23
    Changes: Database references