2YCH

PilM-PilN type IV pilus biogenesis complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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This is version 1.1 of the entry. See complete history


Literature

Structure of the Pilm-Piln Inner Membrane Type Iv Pilus Biogenesis Complex from Thermus Thermophilus.

Karuppiah, V.Derrick, J.P.

(2011) J Biol Chem 286: 24434

  • DOI: 10.1074/jbc.M111.243535
  • Primary Citation of Related Structures:  
    2YCH

  • PubMed Abstract: 
  • Type IV pili are surface-exposed filaments, which extend from a variety of bacterial pathogens and play a major role in pathogenesis, motility, and DNA uptake. Here, we present the crystal structure of a complex between a cytoplasmic component of the type IV pilus biogenesis system from Thermus thermophilus, PilM, in complex with a peptide derived from the cytoplasmic portion of the inner membrane protein PilN ...

    Type IV pili are surface-exposed filaments, which extend from a variety of bacterial pathogens and play a major role in pathogenesis, motility, and DNA uptake. Here, we present the crystal structure of a complex between a cytoplasmic component of the type IV pilus biogenesis system from Thermus thermophilus, PilM, in complex with a peptide derived from the cytoplasmic portion of the inner membrane protein PilN. PilM also binds ATP, and its structure is most similar to the actin-like protein FtsA. PilN binds in a narrow channel between the 1A and 1C subdomains in PilM; the binding site is well conserved in other gram-negative bacteria, notably Neisseria meningitidis, Pseudomonas aeruginosa, and Vibrio cholerae. We find no evidence for the catalysis of ATP hydrolysis by PilM; fluorescence data indicate that the protein is likely to be saturated by ATP at physiological concentrations. In addition, binding of the PilN peptide appears to influence the environment of the ATP binding site. This is the first reported structure of a complex between two type IV pilus biogenesis proteins. We propose a model in which PilM binds ATP and then PilN as one of the first steps in the formation of the inner membrane platform of the type IV pilus biogenesis complex.


    Organizational Affiliation

    Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COMPETENCE PROTEIN PILMA377Thermus thermophilus HB27Mutation(s): 0 
Gene Names: pilMTT_C1013
UniProt
Find proteins for Q72IW8 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72IW8 
Go to UniProtKB:  Q72IW8
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COMPETENCE PROTEIN PILNB15Thermus thermophilus HB27Mutation(s): 0 
Gene Names: pilNTT_C1014
UniProt
Find proteins for Q72IW7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72IW7 
Go to UniProtKB:  Q72IW7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
ATP PDBBind:  2YCH Kd: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.78α = 90
b = 50.78β = 90
c = 366.117γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references, Source and taxonomy, Version format compliance