2V0N | pdb_00002v0n

ACTIVATED RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP AND GTP- ALPHA-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.252 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.215 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of Bef3--Modified Response Regulator Pled: Implications for Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition

Wassmann, P.Chan, C.Paul, R.Beck, A.Heerklotz, H.Jenal, U.Schirmer, T.

(2007) Structure 15: 915

  • DOI: https://doi.org/10.1016/j.str.2007.06.016
  • Primary Citation Related Structures: 
    2V0N

  • PubMed Abstract: 

    Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second messenger involved in the regulation of cell surface-associated traits and persistence. We have determined the crystal structure of PleD from Caulobacter crescentus, a response regulator with a diguanylate cyclase (DGC) domain, in its activated form. The BeF(3)(-) modification of its receiver domain causes rearrangement with respect to an adaptor domain, which, in turn, promotes dimer formation, allowing for the efficient encounter of two symmetric catalytic domains. The substrate analog GTPalphaS and two putative cations are bound to the active sites in a manner similar to adenylate cyclases, suggesting an analogous two-metal catalytic mechanism. An allosteric c-di-GMP-binding mode that crosslinks DGC and an adaptor domain had been identified before. Here, a second mode is observed that crosslinks the DGC domains within a PleD dimer. Both modes cause noncompetitive product inhibition by domain immobilization.


  • Organizational Affiliation
    • Core Program of Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 105.1 kDa 
  • Atom Count: 7,298 
  • Modeled Residue Count: 913 
  • Deposited Residue Count: 918 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RESPONSE REGULATOR PLED
A, B
459Caulobacter vibrioides CB15Mutation(s): 0 
EC: 4.6.1 (PDB Primary Data), 2.7.7.65 (UniProt)
UniProt
Find proteins for B8GZM2 (Caulobacter vibrioides (strain NA1000 / CB15N))
Explore B8GZM2 
Go to UniProtKB:  B8GZM2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8GZM2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E

Query on C2E



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
O [auth B],
P [auth B]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
GAV

Query on GAV



Download:Ideal Coordinates CCD File
G [auth A],
Q [auth B]
GUANOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE
C10 H16 N5 O13 P3 S
YRUWXBKVSXSSGS-KIOICMOXSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
BEF

Query on BEF



Download:Ideal Coordinates CCD File
C [auth A],
M [auth B]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
CL

Query on CL



Download:Ideal Coordinates CCD File
L [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
H [auth A],
I [auth A],
N [auth B],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.252 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.215 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.965α = 90
b = 132.557β = 90
c = 88.425γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-04-03
    Changes: Advisory, Data collection, Other, Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary