3ETE

Crystal structure of bovine glutamate dehydrogenase complexed with hexachlorophene

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Novel Inhibitors Complexed with Glutamate Dehydrogenase: ALLOSTERIC REGULATION BY CONTROL OF PROTEIN DYNAMICS

Li, M., Smith, C.J., Walker, M.T., Smith, T.J.

(2009) J Biol Chem 284: 22988-23000

  • DOI: 10.1074/jbc.M109.020222
  • Primary Citation of Related Structures:  
    3ETD, 3ETE, 3ETG

  • PubMed Abstract: 

    • Mammalian glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate using NAD(P)(+) as coenzyme. Unlike its counterparts from other animal kingdoms, mammalian GDH is regulated by a host of ligands ...

    Mammalian glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate using NAD(P)(+) as coenzyme. Unlike its counterparts from other animal kingdoms, mammalian GDH is regulated by a host of ligands. The recently discovered hyperinsulinism/hyperammonemia disorder showed that the loss of allosteric inhibition of GDH by GTP causes excessive secretion of insulin. Subsequent studies demonstrated that wild-type and hyperinsulinemia/hyperammonemia forms of GDH are inhibited by the green tea polyphenols, epigallocatechin gallate and epicatechin gallate. This was followed by high throughput studies that identified more stable inhibitors, including hexachlorophene, GW5074, and bithionol. Shown here are the structures of GDH complexed with these three compounds. Hexachlorophene forms a ring around the internal cavity in GDH through aromatic stacking interactions between the drug and GDH as well as between the drug molecules themselves. In contrast, GW5074 and bithionol both bind as pairs of stacked compounds at hexameric 2-fold axes between the dimers of subunits. The internal core of GDH contracts when the catalytic cleft closes during enzymatic turnover. None of the drugs cause conformational changes in the contact residues, but all bind to key interfaces involved in this contraction process. Therefore, it seems likely that the drugs inhibit enzymatic turnover by inhibiting this transition. Indeed, this expansion/contraction process may play a major role in the inter-subunit communication and allosteric regulation observed in GDH.

    Organizational Affiliation: 

    Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate dehydrogenaseA, B, C, D, E, F501Bos taurusMutation(s): 0 
Gene Names: GLUD1, GLUD
EC: 1.4.1.3
UniProt
Find proteins for P00366 (Bos taurus)
Explore P00366 
Go to UniProtKB:  P00366
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP
Download Ideal Coordinates CCD File 
 BA [auth F], H [auth A], L [auth B], P [auth C], U [auth D], Y [auth E]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N		 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP
Download Ideal Coordinates CCD File 
 CA [auth F], I [auth A], M [auth B], Q [auth C], V [auth D], Z [auth E]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
H3P (Subject of Investigation/LOI)
Query on H3P
Download Ideal Coordinates CCD File 
 DA [auth F], J [auth A], N [auth B], R [auth C], S [auth C], W [auth D]2,2'-methanediylbis(3,4,6-trichlorophenol)
C13 H6 Cl6 O2
ACGUYXCXAPNIKK-UHFFFAOYSA-N		 Ligand Interaction
GLU
Query on GLU
Download Ideal Coordinates CCD File 
 AA [auth F], G [auth A], K [auth B], O [auth C], T [auth D], X [auth E]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.374α = 90
b = 101.577β = 102.344
c = 166.873γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-10-07 
  • Released Date: 2009-06-09 
    • Deposition Author(s): Li, M., Smith, T.J.

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description