1L5Y

CRYSTAL STRUCTURE OF MG2+ / BEF3-BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain

Park, S.Meyer, M.Jones, A.D.Yennawar, H.P.Yennawar, N.H.Nixon, B.T.

(2002) FASEB J. 16: 1964-1966

  • DOI: 10.1096/fj.02-0395fje
  • Primary Citation of Related Structures:  1L5Z

  • PubMed Abstract: 
  • A Crystallogral structure is described for the Mg2+-BeF3--bound receiver domain of Sinorhizobium meliloti DctD bearing amino acid substitution E121K. Differences between the apo- and ligand-bound active sites are similar to those reported for other r ...

    A Crystallogral structure is described for the Mg2+-BeF3--bound receiver domain of Sinorhizobium meliloti DctD bearing amino acid substitution E121K. Differences between the apo- and ligand-bound active sites are similar to those reported for other receiver domains. However, the off and on states of the DctD receiver domain are characterized by dramatically different dimeric structures, which supports the following hypothesis of signal transduction. In the off state, the receiver domain and coiled-coil linker form a dimer that inhibits oligomerization of the AAA+ ATPase domain. In this conformation, the receiver domain cannot be phosphorylated or bind Mg2+ and BeF3-. Instead, these modifications stabilize an alternative dimeric conformation that repositions the subunits by approximately 20 A, thus replacing the a4-b5-a5 interface with an a4-b5 interface. Reoriented receiver domains permit the ATPase domain to oligomerize and stimulate open complex formation by the s54 form of RNA polymerase. NtrC, which shares 38% sequence identity with DctD, works differently. Its activated receiver domain must facilitate oligomerization of its ATPase domain. Significant differences exist in the signaling surfaces of the DctD and NtrC receiver domains that may help explain how triggering the common two-component switch can variously regulate assembly of a AAA+ ATPase domain.


    Related Citations: 
    • A dimeric two-component receiver domain inhibits the sigma54-dependent ATPase in DctD
      Meyer, M.G.,Park, S.,Zeringue, L.,Staley, M.,McKinstry, M.,Kaufman, R.I.,Zhang, H.,Yan, D.,Yennawar, N.,Yennawar, H.,Farber, G.K.,Nixon, B.T.
      (2001) FASEB J. 15: 1326


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
A, B
155Rhizobium meliloti (strain 1021)Gene Names: dctD
Find proteins for P13632 (Rhizobium meliloti (strain 1021))
Go to UniProtKB:  P13632
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BF2
Query on BF2

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Download CCD File 
A, B
BERYLLIUM DIFLUORIDE
Be F2
JZKFIPKXQBZXMW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BF4
Query on BF4

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Download CCD File 
A
BERYLLIUM TETRAFLUORIDE ION
Be F4
UUMYFIKVCFICLB-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

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Download CCD File 
A, B
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.005α = 90.00
b = 76.837β = 90.00
c = 77.853γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata scaling
d*TREKdata reduction
CNSrefinement
CrystalCleardata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence