5YIV

Caulobacter crescentus GcrA DNA-binding domain(DBD) in complex with methylated dsDNA(crystal form 1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.914 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.

Wu, X.Haakonsen, D.L.Sanderlin, A.G.Liu, Y.J.Shen, L.Zhuang, N.Laub, M.T.Zhang, Y.

(2018) Nucleic Acids Res. 46: 3245-3256

  • DOI: 10.1093/nar/gky161
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Canonical bacterial transcription activators bind to non-transcribed promoter elements to increase transcription of their target genes. Here we report crystal structures of binary complexes comprising domains of Caulobacter crescentus GcrA, a noncano ...

    Canonical bacterial transcription activators bind to non-transcribed promoter elements to increase transcription of their target genes. Here we report crystal structures of binary complexes comprising domains of Caulobacter crescentus GcrA, a noncanonical bacterial transcription factor, that support a novel mechanism for transcription activation through the preferential binding of methylated cis-regulatory elements and the promotion of open complex formation through an interaction with region 2 of the principal σ factor, σ70. We present crystal structures of the C-terminal, σ factor-interacting domain (GcrA-SID) in complex with domain 2 of σ70 (σ702), and the N-terminal, DNA-binding domain (GcrA-DBD) in complex with methylated double-stranded DNA (dsDNA). The structures reveal interactions essential for transcription activation and DNA recognition by GcrA. These structures, along with mutational analyses, support a mechanism of transcription activation in which GcrA associates with RNA polymerase (RNAP) prior to promoter binding through GcrA-SID, arming RNAP with a flexible GcrA-DBD. The RNAP-GcrA complex then binds and activates target promoters harboring a methylated GcrA binding site either upstream or downstream of the transcription start site.


    Organizational Affiliation

    Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell cycle regulatory protein GcrA
A, B, C, D
49Caulobacter vibrioides (strain NA1000 / CB15N)Gene Names: gcrA
Find proteins for A0A0H3C9J4 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3C9J4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3')E,G,I,K9synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3')F,H,J,L9synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MA
Query on 6MA
E, F, G, H, I, J, K, L
DNA LINKINGC11 H16 N5 O6 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.914 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.017α = 90.00
b = 131.704β = 90.00
c = 77.664γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-10-06 
  • Released Date: 2018-03-21 
  • Deposition Author(s): Wu, X., Zhang, Y.

Funding OrganizationCountryGrant Number
National Natural Science Foundation of ChinaChina31670067

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references