2YOC | pdb_00002yoc

Crystal structure of PulA from Klebsiella oxytoca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 
    0.213 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2YOC

This is version 1.4 of the entry. See complete history

Literature

Structural Basis of Pullulanase Membrane Binding and Secretion Revealed by X-Ray Crystallography, Molecular Dynamics and Biochemical Analysis

East, A.Mechaly, A.E.Huysmans, G.H.M.Bernarde, C.Tello-Manigne, D.Nadeau, N.Pugsley, A.P.Buschiazzo, A.Alzari, P.M.Bond, P.J.Francetic, O.

(2016) Structure 24: 92

  • DOI: https://doi.org/10.1016/j.str.2015.10.023
  • Primary Citation Related Structures: 
    2YOC

  • PubMed Abstract: 

    The Klebsiella lipoprotein pullulanase (PulA) is exported to the periplasm, triacylated, and anchored via lipids in the inner membrane (IM) prior to its transport to the bacterial surface through a type II secretion system (T2SS). X-Ray crystallography and atomistic molecular dynamics (MD) simulations of PulA in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) model membrane provided an unprecedented molecular view of an N-terminal unstructured tether and the IM lipoprotein retention signal, and revealed novel interactions with the IM via N-terminal immunoglobulin-like domains in PulA. An efficiently secreted nonacylated variant (PulANA) showed similar peripheral membrane association during MD simulations, consistent with the binding of purified PulANA to liposomes. Remarkably, combined X-ray, MD, and functional studies identified a novel subdomain, Ins, inserted in the α-amylase domain, which is required for PulA secretion. Available data support a model in which PulA binding to the IM promotes interactions with the T2SS, possibly via the Ins subdomain.


  • Organizational Affiliation
    • Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Macromolecule Content 

  • Total Structure Weight: 238.22 kDa 
  • Atom Count: 16,490 
  • Modeled Residue Count: 2,106 
  • Deposited Residue Count: 2,156 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PULLULANASE
A, B
1,078Klebsiella oxytocaMutation(s): 0 
EC: 3.2.1.41
Membrane Entity: Yes 
UniProt
Find proteins for P07206 (Klebsiella pneumoniae)
Explore P07206 
Go to UniProtKB:  P07206
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07206
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
O [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
K [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free:  0.213 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 179.15α = 90
b = 179.15β = 90
c = 334.69γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2015-12-23
    Changes: Database references
  • Version 1.2: 2016-01-13
    Changes: Database references
  • Version 1.3: 2016-01-20
    Changes: Database references
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary