3NBX

Crystal structure of E. coli RavA (Regulatory ATPase variant A) in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity

El Bakkouri, M.Gutsche, I.Kanjee, U.Zhao, B.Yu, M.Goret, G.Schoehn, G.Burmeister, W.P.Houry, W.A.

(2010) Proc Natl Acad Sci U S A 107: 22499-22504

  • DOI: 10.1073/pnas.1009092107
  • Primary Citation of Related Structures:  
    3NBX

  • PubMed Abstract: 
  • The MoxR family of AAA+ ATPases is widespread throughout bacteria and archaea but remains poorly characterized. We recently found that the Escherichia coli MoxR protein, RavA (Regulatory ATPase variant A), tightly interacts with the inducible lysine ...

    The MoxR family of AAA+ ATPases is widespread throughout bacteria and archaea but remains poorly characterized. We recently found that the Escherichia coli MoxR protein, RavA (Regulatory ATPase variant A), tightly interacts with the inducible lysine decarboxylase, LdcI/CadA, to form a unique cage-like structure. Here, we present the X-ray structure of RavA and show that the αβα and all-α subdomains in the RavA AAA+ module are arranged as in magnesium chelatases rather than as in classical AAA+ proteins. RavA structure also contains a discontinuous triple-helical domain as well as a β-barrel-like domain forming a unique fold, which we termed the LARA domain. The LARA domain was found to mediate the interaction between RavA and LdcI. The RavA structure provides insights into how five RavA hexamers interact with two LdcI decamers to form the RavA-LdcI cage-like structure.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATPase ravAX500Escherichia coli K-12Mutation(s): 0 
Gene Names: b3746JW3725ravAyieN
EC: 3.6.3
Find proteins for P31473 (Escherichia coli (strain K12))
Explore P31473 
Go to UniProtKB:  P31473
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
X
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
X
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.232α = 90
b = 162.232β = 90
c = 55.316γ = 120
Software Package:
Software NamePurpose
DNAdata collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-06-04 
  • Released Date: 2011-01-12 
  • Deposition Author(s): El Bakkouri, M.

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-11-12
    Changes: Structure summary