1JE8

Two-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dimerization allows DNA target site recognition by the NarL response regulator.

Maris, A.E.Sawaya, M.R.Kaczor-Grzeskowiak, M.Jarvis, M.R.Bearson, S.M.Kopka, M.L.Schroder, I.Gunsalus, R.P.Dickerson, R.E.

(2002) Nat.Struct.Mol.Biol. 9: 771-778

  • DOI: 10.1038/nsb845

  • PubMed Abstract: 
  • Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component ...

    Two-component signal transduction systems are modular phosphorelay regulatory pathways common in prokaryotes. In the co-crystal structure of the Escherichia coli NarL signal output domain bound to DNA, we observe how the NarL family of two-component response regulators can bind DNA. DNA recognition is accompanied by the formation of a new dimerization interface, which could occur only in the full-length protein via a large intramolecular domain rearrangement. The DNA is recognized by the concerted effects of solvation, van der Waals forces and inherent DNA deformability, rather than determined primarily by major groove hydrogen bonding. These subtle forces permit a small DNA-binding domain to perturb the DNA helix, leading to major DNA curvature and a transition from B- to A-form DNA at the binding site, where valine on the recognition helix interacts unexpectedly with the polar major groove floor.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, P.O. Box 951569, Los Angeles, California 90095-1569, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nitrate/Nitrite Response Regulator Protein NARL
A, B, E, F
82Escherichia coli (strain K12)Gene Names: narL (frdR)
Find proteins for P0AF28 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AF28
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'C,D,G,H20N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 0.15 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.257α = 90.00
b = 52.741β = 90.00
c = 83.863γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
GLRFphasing
CCP4data scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-09-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance