6AG5 | pdb_00006ag5

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

• PDB DOI: https://doi.org/10.2210/pdb6AG5/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-08-09 Released: 2019-08-14 
• Deposition Author(s): Chang, Y.Y., Hsu, C.H.
• Funding Organization(s): Ministry of Science and Technology (Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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

• PubMed: 32780067 
• DOI: https://doi.org/10.1039/d0cc04305b
• Primary Citation of Related Structures:  
  6AG4, 6AG5


• 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. 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.

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Organizational Affiliation: 

Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 21.36 kDa 
• Atom Count: 1,443 
• Modelled Residue Count: 157 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-alpha-acetyltransferase	A	175	Saccharolobus solfataricus P2	Mutation(s): 2  Gene Names: AsArd1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	B [auth A]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.217	α = 90
b = 52.926	β = 90
c = 73.576	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	103-2113-M-002 -009 -MY2

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description