2YJT

Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Potential Regulatory Interactions of Escherichia Coli Rraa Protein with Dead-Box Helicases.

Pietras, Z., Hardwick, S.W., Swiezewski, S., Luisi, B.F.

(2013) J Biol Chem 288: 31919

  • DOI: 10.1074/jbc.M113.502146
  • Primary Citation of Related Structures:  
    2YJT, 2YJV

  • PubMed Abstract: 

    • Members of the DEAD-box family of RNA helicases contribute to virtually every aspect of RNA metabolism, in organisms from all domains of life. Many of these helicases are constituents of multicomponent assemblies, and their interactions with partner proteins within the complexes underpin their activities and biological function ...

    Members of the DEAD-box family of RNA helicases contribute to virtually every aspect of RNA metabolism, in organisms from all domains of life. Many of these helicases are constituents of multicomponent assemblies, and their interactions with partner proteins within the complexes underpin their activities and biological function. In Escherichia coli the DEAD-box helicase RhlB is a component of the multienzyme RNA degradosome assembly, and its interaction with the core ribonuclease RNase E boosts the ATP-dependent activity of the helicase. Earlier studies have identified the regulator of ribonuclease activity A (RraA) as a potential interaction partner of both RNase E and RhlB. We present structural and biochemical evidence showing how RraA can bind to, and modulate the activity of RhlB and another E. coli DEAD-box enzyme, SrmB. Crystallographic structures are presented of RraA in complex with a portion of the natively unstructured C-terminal tail of RhlB at 2.8-Å resolution, and in complex with the C-terminal RecA-like domain of SrmB at 2.9 Å. The models suggest two distinct mechanisms by which RraA might modulate the activity of these and potentially other helicases.

    Organizational Affiliation: 

    From the Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom and.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
REGULATOR OF RIBONUCLEASE ACTIVITY AA, B, C161Escherichia coli K-12Mutation(s): 0 
Gene Names: rraA, menG, yiiV, b3929, JW3900
UniProt
Find proteins for P0A8R0 (Escherichia coli (strain K12))
Explore P0A8R0 
Go to UniProtKB:  P0A8R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8R0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-DEPENDENT RNA HELICASE SRMBD170Escherichia coli K-12Mutation(s): 0 
Gene Names: srmB, rbaB, rhlA, b2576, JW2560
EC: 3.6.4.13
UniProt
Find proteins for P21507 (Escherichia coli (strain K12))
Explore P21507 
Go to UniProtKB:  P21507
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21507
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.39α = 90
b = 73.39β = 90
c = 222.891γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2013-11-13
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Changes: Data collection, Experimental preparation