5C88

Crystal structure of Ard1 N-terminal acetyltransferase from Sulfolobus solfataricus in monoclinic form

• PDB DOI: https://doi.org/10.2210/pdb5C88/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2015-06-25 Released: 2016-01-13 
• Deposition Author(s): Chang, Y.Y., Hsu, C.H.
• Funding Organization(s): Ministry of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.265 
• R-Value Work: 0.161 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Multiple Conformations of the Loop Region Confers Heat-Resistance on SsArd1, a Thermophilic NatA.

Chang, Y.Y., Hsu, C.H.

(2016) Chembiochem 17: 214-217

• PubMed: 26593285 
• DOI: https://doi.org/10.1002/cbic.201500568
• Primary Citation of Related Structures:  
  5C88


• PubMed Abstract: 
  

  Structural comparison indicates that the loop region between β3 and β4 of SsArd1 is extended relative to the corresponding region in mesophilic Nats, and forms a plastic hydrogen-bond network mainly at two serine residues. Strikingly, two single-point mutants showed ∼3 °C decrease in melting temperature, and two other variants showed ∼7 °C decrease; this correlated with significantly reduced enzymatic activity. To our knowledge, this is the first discovery of a loop region capable of remarkably improving protein thermostability. This provides a novel route to engineer heat-resistant proteins.

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Organizational Affiliation: 

Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 42.14 kDa 
• Atom Count: 2,718 
• Modelled Residue Count: 315 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized N-acetyltransferase SSO0209	A, B	173	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: SSO0209 EC: 2.3.1.88
UniProt
Find proteins for Q980R9 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q980R9  Go to UniProtKB:  Q980R9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.265 
• R-Value Work: 0.161 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.154	α = 90
b = 84.246	β = 89.88
c = 49.165	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data processing
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Chang, Y.Y., Hsu, C.H.

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

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description