Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D5  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 412.81 kDa 
• Atom Count: 32266 
• Modelled Residue Count: 3555 
• Deposited Residue Count: 3575 
• Unique protein chains: 1

3N75

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

• PDB DOI: 10.2210/pdb3N75/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-26 Released: 2011-02-16 
• Deposition Author(s): Kanjee, U., Alexopoulos, E., Pai, E.F., Houry, W.A.

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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 

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

• PubMed: 21278708 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine decarboxylase, inducible	A, B, C, D, E	715	Escherichia coli K-12	Mutation(s): 0  Gene Names: b4131, cadA, JW4092, ldcI, LdcI/CadA EC: 4.1.1.18
UniProt
Find proteins for P0A9H3 (Escherichia coli (strain K12)) Explore P0A9H3  Go to UniProtKB:  P0A9H3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P	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
P6G	G [auth A], J [auth B], M [auth C], P [auth D], S [auth E]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
GOL	H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D, E	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Binding Affinity Annotations
ID	Source	Binding 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 = 271.76	α = 90
b = 181.993	β = 125.41
c = 170.902	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-26 
• Released Date: 2011-02-16 
Deposition Author(s): Kanjee, U., Alexopoulos, E., Pai, E.F., Houry, W.A.

Revision History  

• 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