6AIC

Crystal structures of the N-terminal domain of Staphylococcus aureus DEAD-box Cold shock RNA helicase CshA in complex with AMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of the N-terminal domain of the Staphylococcus aureus DEAD-box RNA helicase CshA and its complex with AMP

Chen, X.Wang, C.Zhang, X.Tian, T.Zang, J.

(2018) Acta Crystallogr F Struct Biol Commun 74: 704-709

  • DOI: https://doi.org/10.1107/S2053230X1801292X
  • Primary Citation of Related Structures:  
    6AIB, 6AIC

  • PubMed Abstract: 

    CshA is a DEAD-box RNA helicase that belongs to the DExD/H-box family of proteins, which generally have an RNA-dependent ATPase activity. In Staphylococcus aureus, CshA was identified as a component of the RNA degradosome and plays important roles in RNA turnover. In this study, the crystal structures of the N-terminal RecA-like domain 1 of S. aureus CshA (SaCshA R1 ) and of its complex with AMP (SaCshA R1 -AMP) are reported at resolutions of 1.5 and 1.8 Å, respectively. SaCshA R1 adopts a conserved α/β RecA-like structure with seven parallel strands surrounded by nine α-helices. The Q motif and motif I are responsible for the binding of the adenine group and phosphate group of AMP, respectively. Structure comparison of SaCshA R1 -AMP and SaCshA R1 reveals that motif I undergoes a conformational change upon AMP binding. Isothermal titration calorimetry assays further conformed the essential roles of Phe22 in the Q motif and Lys52 in motif I for binding ATP, indicating a conserved substrate-binding mechanism in SaCshA compared with other DEAD-box RNA helicases.


  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, Collaborative Innovation Center of Chemistry for Life Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DEAD-box ATP-dependent RNA helicase CshA214Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Gene Names: cshASAR2168
EC: 3.6.4.13
UniProt
Find proteins for Q6GEZ3 (Staphylococcus aureus (strain MRSA252))
Explore Q6GEZ3 
Go to UniProtKB:  Q6GEZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GEZ3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.386α = 90
b = 52.183β = 118.53
c = 44.419γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references