3N75

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


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:  
    3N75, 3Q16

  • 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 processes underlying the acid stress response, the X-ray crystal structure of LdcI was determined ...

    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 Struct Biol Cryst Commun 64(8): 700

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine decarboxylase, inducibleA, B, C, D, E715Escherichia coli K-12Mutation(s): 0 
Gene Names: b4131cadAJW4092ldcILdcI/CadA
EC: 4.1.1.18
UniProt
Find proteins for P0A9H3 (Escherichia coli (strain K12))
Explore P0A9H3 
Go to UniProtKB:  P0A9H3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9H3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4P
Query on G4P

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
O [auth D],
R [auth E]
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-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
Binding Affinity Annotations 
IDSourceBinding Affinity
G4P Binding MOAD:  3N75 Kd: 12.8 (nM) from 1 assay(s)
PDBBind:  3N75 Kd: 12.8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 271.76α = 90
b = 181.993β = 125.41
c = 170.902γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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