2DGM

Crystal structure of Escherichia coli GadB in complex with iodide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Escherichia coli acid resistance: pH-sensing, activation by chloride and autoinhibition in GadB

Gut, H.Pennacchietti, E.John, R.A.Bossa, F.Capitani, G.De Biase, D.Gruetter, M.G.

(2006) EMBO J 25: 2643-2651

  • DOI: 10.1038/sj.emboj.7601107
  • Primary Citation of Related Structures:  
    2DGK, 2DGL, 2DGM

  • PubMed Abstract: 
  • Escherichia coli and other enterobacteria exploit the H+ -consuming reaction catalysed by glutamate decarboxylase to survive the stomach acidity before reaching the intestine. Here we show that chloride, extremely abundant in gastric secretions, is an allosteric activator producing a 10-fold increase in the decarboxylase activity at pH 5 ...

    Escherichia coli and other enterobacteria exploit the H+ -consuming reaction catalysed by glutamate decarboxylase to survive the stomach acidity before reaching the intestine. Here we show that chloride, extremely abundant in gastric secretions, is an allosteric activator producing a 10-fold increase in the decarboxylase activity at pH 5.6. Cooperativity and sensitivity to chloride were lost when the N-terminal 14 residues, involved in the formation of two triple-helix bundles, were deleted by mutagenesis. X-ray structures, obtained in the presence of the substrate analogue acetate, identified halide-binding sites at the base of each N-terminal helix, showed how halide binding is responsible for bundle stability and demonstrated that the interconversion between active and inactive forms of the enzyme is a stepwise process. We also discovered an entirely novel structure of the cofactor pyridoxal 5'-phosphate (aldamine) to be responsible for the reversibly inactivated enzyme. Our results link the entry of chloride ions, via the H+/Cl- exchange activities of ClC-ec1, to the trigger of the acid stress response in the cell when the intracellular proton concentration has not yet reached fatal values.


    Related Citations: 
    • Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase
      Capitani, G., De Biase, D., Aurizi, C., Gut, H., Bossa, F., Gruetter, M.G.
      (2003) EMBO J 22: 4027

    Organizational Affiliation

    Biochemisches Institut der Universität Zürich, Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate decarboxylase beta
A, B, C, D, E, F
A, B, C, D, E, F
466Escherichia coliMutation(s): 0 
Gene Names: gadB
EC: 4.1.1.15
UniProt
Find proteins for P69910 (Escherichia coli (strain K12))
Explore P69910 
Go to UniProtKB:  P69910
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69910
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
CA [auth C],
CB [auth F],
KA [auth D],
M [auth A],
TA [auth E],
CA [auth C],
CB [auth F],
KA [auth D],
M [auth A],
TA [auth E],
W [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth C],
AB [auth F],
BA [auth C],
BB [auth F],
EA [auth D],
AA [auth C],
AB [auth F],
BA [auth C],
BB [auth F],
EA [auth D],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
OA [auth E],
PA [auth E],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
SA [auth E],
T [auth B],
U [auth B],
V [auth B],
XA [auth F],
Y [auth C],
YA [auth F],
Z [auth C],
ZA [auth F]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
WA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
VA [auth E]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
DA [auth C],
DB [auth F],
EB [auth F],
FB [auth F],
GB [auth F],
DA [auth C],
DB [auth F],
EB [auth F],
FB [auth F],
GB [auth F],
LA [auth D],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
P [auth A],
UA [auth E],
X [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.227 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.336α = 76.65
b = 91.804β = 76.94
c = 93.914γ = 78.04
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance