6SLJ

Structure of the RagAB peptide transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation 3D Report Full Report



Literature

Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.

Madej, M.White, J.B.R.Nowakowska, Z.Rawson, S.Scavenius, C.Enghild, J.J.Bereta, G.P.Pothula, K.Kleinekathoefer, U.Basle, A.Ranson, N.A.Potempa, J.van den Berg, B.

(2020) Nat Microbiol 

  • DOI: 10.1038/s41564-020-0716-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated pepti ...

    Porphyromonas gingivalis, an asaccharolytic member of the Bacteroidetes, is a keystone pathogen in human periodontitis that may also contribute to the development of other chronic inflammatory diseases. P. gingivalis utilizes protease-generated peptides derived from extracellular proteins for growth, but how these peptides enter the cell is not clear. Here, we identify RagAB as the outer-membrane importer for these peptides. X-ray crystal structures show that the transporter forms a dimeric RagA 2 B 2 complex, with the RagB substrate-binding surface-anchored lipoprotein forming a closed lid on the RagA TonB-dependent transporter. Cryo-electron microscopy structures reveal the opening of the RagB lid and thus provide direct evidence for a 'pedal bin' mechanism of nutrient uptake. Together with mutagenesis, peptide-binding studies and RagAB peptidomics, our work identifies RagAB as a dynamic, selective outer-membrane oligopeptide-acquisition machine that is essential for the efficient utilization of proteinaceous nutrients by P. gingivalis.


    Organizational Affiliation

    Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, UK. bert.van-den-berg@ncl.ac.uk.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RagA protein
A, B
997Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: ragAPG_0185
Find proteins for Q7MXJ7 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  Q7MXJ7

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein RagB
C, D
488Porphyromonas gingivalis W83Mutation(s): 0 
Gene Names: ragBPG_0186
Find proteins for F5H948 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  F5H948
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ALA-SER-THR-THR-GLY-ALA-ASN-SER-GLN-ARG-GLY-SER-GLY
P
13Porphyromonas gingivalis W83Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ALA-SER-THR-THR-GLY-ALA-ASN-SER-GLN-ARG
Q
10Porphyromonas gingivalis W83Mutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download CCD File 
A, B
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
LMT
Query on LMT

Download CCD File 
A, B, C
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
C8E
Query on C8E

Download CCD File 
A, B
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
PLM
Query on PLM

Download CCD File 
C, D
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.597α = 90
b = 142.021β = 90
c = 241.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-20
    Type: Initial release