3N75

X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.

Kanjee, U.Gutsche, I.Alexopoulos, E.Zhao, B.El Bakkouri, M.Thibault, G.Liu, K.Ramachandran, S.Snider, J.Pai, E.F.Houry, W.A.

(2011) Embo J. 30: 931-944

  • DOI: 10.1038/emboj.2011.5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH∼5). To gain a better understanding of the molecular ...

    The Escherichia coli inducible lysine decarboxylase, LdcI/CadA, together with the inner-membrane lysine-cadaverine antiporter, CadB, provide cells with protection against mild acidic conditions (pH∼5). To gain a better understanding of the molecular processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined. The structure revealed that the protein is an oligomer of five dimers that associate to form a decamer. Surprisingly, LdcI was found to co-crystallize with the stringent response effector molecule ppGpp, also known as the alarmone, with 10 ppGpp molecules in the decamer. ppGpp is known to mediate the stringent response, which occurs in response to nutrient deprivation. The alarmone strongly inhibited LdcI enzymatic activity. This inhibition is important for modulating the consumption of lysine in cells during acid stress under nutrient limiting conditions. Hence, our data provide direct evidence for a link between the bacterial acid stress and stringent responses.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of the inducible lysine decarboxylase from Escherichia coli.
      Alexopoulos, E.,Kanjee, U.,Snider, J.,Houry, W.A.,Pai, E.F.
      (2008) Acta Crystallogr.,Sect.F 64(8): 700


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysine decarboxylase, inducible
A, B, C, D, E
715Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: cadA (ldcI)
EC: 4.1.1.18
Find proteins for P0A9H3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A9H3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
G4P
Query on G4P

Download SDF File 
Download CCD File 
A, B, C, D, E
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A, B, C, D, E
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B, C, D, E
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G4PKd: 685 nM BINDINGMOAD
G4PKd: 12.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 271.760α = 90.00
b = 181.993β = 125.41
c = 170.902γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Source and taxonomy