6EUD

Crystal structure of E. coli DExH-box NTPase HrpB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of the Escherichia coli DExH-Box NTPase HrpB.

Pietrzyk-Brzezinska, A.J.Absmeier, E.Klauck, E.Wen, Y.Antelmann, H.Wahl, M.C.

(2018) Structure 26: 1462-1473.e4

  • DOI: 10.1016/j.str.2018.07.013

  • PubMed Abstract: 
  • Eukaryotic DExH-box proteins are important post-transcriptional gene regulators, many of which employ RNA-stimulated nucleoside triphosphatase activity to remodel RNAs or ribonucleoprotein complexes. However, bacterial DExH-box proteins are structura ...

    Eukaryotic DExH-box proteins are important post-transcriptional gene regulators, many of which employ RNA-stimulated nucleoside triphosphatase activity to remodel RNAs or ribonucleoprotein complexes. However, bacterial DExH-box proteins are structurally and functionally poorly characterized. We report the crystal structure of the Escherichia coli DExH-box protein HrpB. A globular head is composed of dual RecA, winged-helix, helical bundle and oligonucleotide/oligosaccharide-binding domains, resembling a compact version of eukaryotic DExH-box proteins. Additionally, HrpB harbors a C-terminal region not found in proteins with known structure, which bestows the protein with unique interaction potential. Interaction and activity assays showed that the protein binds RNA but not DNA, hydrolyzes all nucleoside triphosphates in an RNA-stimulated manner, but does not unwind diverse model RNAs in vitro. These observations can be rationalized by detailed comparisons with structurally characterized eukaryotic DExH-box proteins. Comparative phenotypic analyses of an E. coli hrpB knockout mutant suggested diverse functions of HrpB homologs in different bacteria.


    Organizational Affiliation

    Freie Universität Berlin, Laboratory of Structural Biochemistry, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent RNA helicase HrpB
A
812Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: hrpB (yadO)
EC: 3.6.4.13
Find proteins for P37024 (Escherichia coli (strain K12))
Go to UniProtKB:  P37024
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.710α = 90.00
b = 131.410β = 90.00
c = 166.110γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
AutoSolphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alexander von Humboldt FoundationGermanyPOL 1161176 STP

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Data collection, Database references