1L5Y

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/10.1096/fj.02-0395fje
  • Primary Citation of Related Structures:  
    1L5Y, 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
A, B
155Sinorhizobium melilotiMutation(s): 1 
Gene Names: dctD
UniProt
Find proteins for P13632 (Rhizobium meliloti (strain 1021))
Explore P13632 
Go to UniProtKB:  P13632
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13632
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
Q [auth B],
R [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
W [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BF4
Query on BF4

Download Ideal Coordinates CCD File 
O [auth A]BERYLLIUM TETRAFLUORIDE ION
Be F4
UUMYFIKVCFICLB-UHFFFAOYSA-J
BEF
Query on BEF

Download Ideal Coordinates CCD File 
F [auth A],
S [auth B],
V [auth B]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
BF2
Query on BF2

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
T [auth B],
U [auth B]
BERYLLIUM DIFLUORIDE
Be F2
JZKFIPKXQBZXMW-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
P [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 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
b = 76.837β = 90
c = 77.853γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
AMoREphasing
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-23
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description