8PO7 | pdb_00008po7

Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.

Xin, B.G.Huang, L.Y.Yuan, L.G.Liu, N.N.Li, H.H.Ai, X.Lei, D.S.Hou, X.M.Rety, S.Xi, X.G.

(2024) Nucleic Acids Res 52: 3406-3418

  • DOI: https://doi.org/10.1093/nar/gkae138
  • Primary Citation of Related Structures:  
    8PO6, 8PO7, 8PO8

  • PubMed Abstract: 

    RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.


  • Organizational Affiliation

    College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase HrpA
A, B
758Escherichia coli K-12Mutation(s): 0 
Gene Names: hrpAb1413JW5905
EC: 3.6.4.13
UniProt
Find proteins for P43329 (Escherichia coli (strain K12))
Explore P43329 
Go to UniProtKB:  P43329
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43329
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.47α = 90
b = 106.124β = 90
c = 178.276γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870788
Other governmentZ101021903

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Derived calculations