3PXP

Crystal structure of a PAS and DNA binding domain containing protein (Caur_2278) from CHLOROFLEXUS AURANTIACUS J-10-FL at 2.30 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structure of an MmyB-Like Regulator from C. aurantiacus, Member of a New Transcription Factor Family Linked to Antibiotic Metabolism in Actinomycetes.

Xu, Q.van Wezel, G.P.Chiu, H.J.Jaroszewski, L.Klock, H.E.Knuth, M.W.Miller, M.D.Lesley, S.A.Godzik, A.Elsliger, M.A.Deacon, A.M.Wilson, I.A.

(2012) PLoS One 7: e41359-e41359

  • DOI: 10.1371/journal.pone.0041359
  • Primary Citation of Related Structures:  
    3PXP

  • PubMed Abstract: 
  • Actinomycetes are important bacterial sources of antibiotics and other secondary metabolites. Many antibiotic gene clusters are controlled by pathway-specific activators that act in response to growth conditions. Here we present the crystal structure of an MmyB-like transcription regulator MltR (PDB code 3pxp) (Caur_2278) from Chloroflexus aurantiacus, in complex with a fatty acid (myristic acid) ...

    Actinomycetes are important bacterial sources of antibiotics and other secondary metabolites. Many antibiotic gene clusters are controlled by pathway-specific activators that act in response to growth conditions. Here we present the crystal structure of an MmyB-like transcription regulator MltR (PDB code 3pxp) (Caur_2278) from Chloroflexus aurantiacus, in complex with a fatty acid (myristic acid). MltR is a distant homolog of the methylenomycin activator MmyB and consists of an Xre-type N-terminal DNA-binding domain and a C-terminal ligand-binding module that is related to the Per-Arnt-Sim (PAS) domain. This structure has enabled identification of a new family of bacterial transcription factors that are distributed predominantly in actinomycetes. Bioinformatics analysis of MltR and other characterized family members suggest that they are likely associated with antibiotic and fatty acid metabolism in actinomycetes. Streptomyces coelicolor SCO4944 is a candidate as an ancestral member of the family. Its ortholog in S. griseus, SGR_6891, is induced by A-factor, a γ-butyrolactone that controls antibiotic production and development, and is adjacent to the A-factor synthase gen, afsA. The location of mltR/mmyB homologs, in particular those adjacent to less well-studied antibiotic-related genes, makes them interesting genetic markers for identifying new antibiotic genes. A model for signal-triggered DNA-binding by MltR is proposed.


    Organizational Affiliation

    Joint Center for Structural Genomics, La Jolla, California, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Helix-turn-helix domain proteinA, B, C292Chloroflexus aurantiacus J-10-flMutation(s): 0 
Gene Names: Caur_2278
UniProt
Find proteins for A9WGF5 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl))
Explore A9WGF5 
Go to UniProtKB:  A9WGF5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR (Subject of Investigation/LOI)
Query on MYR

Download Ideal Coordinates CCD File 
D [auth A], J [auth B], O [auth C]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , N [auth B] , S [auth C] , 
F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], S [auth C], T [auth C], U [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A], K [auth B], P [auth C], Q [auth C], R [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, CL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.807α = 90
b = 83.568β = 103.12
c = 54.52γ = 90
Software Package:
Software NamePurpose
SHELXphasing
BUSTER-TNTrefinement
XSCALEdata processing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Structure summary
  • Version 1.3: 2012-08-15
    Changes: Database references
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence