4AUI

STRUCTURE AND FUNCTION OF THE PORB PORIN FROM DISSEMINATING N. GONORRHOEAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Function of the Porb Porin from Disseminating Neisseria Gonorrhoeae.

Zeth, K.Kozjak-Pavlovic, V.Faulstich, M.Fraunholz, M.Hurwitz, R.Kepp, O.Rudel, T.

(2013) Biochem.J. 449: 631

  • DOI: 10.1042/BJ20121025

  • PubMed Abstract: 
  • The outer membrane of Gram-negative bacteria contains a large number of channel-forming proteins, porins, for the uptake of small nutrient molecules. Neisseria gonorrhoeae PorBIA (PorB of serotype A) are associated with disseminating diseases and med ...

    The outer membrane of Gram-negative bacteria contains a large number of channel-forming proteins, porins, for the uptake of small nutrient molecules. Neisseria gonorrhoeae PorBIA (PorB of serotype A) are associated with disseminating diseases and mediate a rapid bacterial invasion into host cells in a phosphate-sensitive manner. To gain insights into this structure-function relationship we analysed PorBIA by X-ray crystallography in the presence of phosphate and ATP. The structure of PorBIA in the complex solved at a resolution of 3.3 Å (1 Å=0.1 nm) displays a surplus of positive charges inside the channel. ATP ligand-binding in the channel is co-ordinated by the positively charged residues of the channel interior. These residues ligate the aromatic, sugar and pyrophosphate moieties of the ligand. Two phosphate ions were observed in the structure, one of which clamped by two arginine residues (Arg92 and Arg124) localized at the extraplasmic channel exit. A short β-bulge in β2-strand together with the long L3 loop narrow the barrel diameter significantly and further support substrate specificity through hydrogen bond interactions. Interestingly the structure also comprised a small peptide as a remnant of a periplasmic protein which physically links porin molecules to the peptidoglycan network. To test the importance of Arg92 on bacterial invasion the residue was mutated. In vivo assays of bacteria carrying a R92S mutation confirmed the importance of this residue for host-cell invasion. Furthermore systematic sequence and structure comparisons of PorBIA from Neisseriaceae indicated Arg92 to be unique in disseminating N. gonorrhoeae thereby possibly distinguishing invasion-promoting porins from other neisserial porins.


    Organizational Affiliation

    Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany. kornelius.zeth@googlemail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PORIN (PORB)
A, B, C
327Neisseria gonorrhoeaeGene Names: porB
Find proteins for Q51056 (Neisseria gonorrhoeae)
Go to UniProtKB:  Q51056
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
POLY ALA
D, E, F
8N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.050α = 90.00
b = 111.470β = 102.07
c = 88.340γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2012-11-14
    Type: Database references
  • Version 1.2: 2013-01-23
    Type: Database references