5XWC

Crystal Structure of Aspergillus niger Glutamate Dehydrogenase Complexed With Alpha-iminoglutarate, 2-amino-2-hydroxyglutarate and NADP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

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Literature

Structural basis for the catalytic mechanism and alpha-ketoglutarate cooperativity of glutamate dehydrogenase.

Prakash, P., Punekar, N.S., Bhaumik, P.

(2018) J Biol Chem 293: 6241-6258

  • DOI: https://doi.org/10.1074/jbc.RA117.000149
  • Primary Citation of Related Structures:  
    5XVI, 5XVV, 5XVX, 5XW0, 5XWC

  • PubMed Abstract: 

    • Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete ...

    Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP + -dependent allosteric enzyme that is forward-inhibited by the formation of mixed disulfide. We determined the structures of the active enzyme in its apo form and in binary/ternary complexes with bound substrate (α-ketoglutarate), inhibitor (isophthalate), coenzyme (NADPH), or two reaction intermediates (α-iminoglutarate and 2-amino-2-hydroxyglutarate). The structure of the forward-inhibited enzyme (fiAnGDH) was also determined. The hexameric AnGDH had three open subunits at one side and three partially closed protomers at the other, a configuration not previously reported. The AnGDH hexamers having subunits with different conformations indicated that its α-ketoglutarate-dependent homotropic cooperativity follows the Monod-Wyman-Changeux (MWC) model. Moreover, the position of the water attached to Asp-154 and Gly-153 defined the previously unresolved ammonium ion-binding pocket, and the binding site for the 2'-phosphate group of the coenzyme was also better defined by our structural data. Additional structural and mutagenesis experiments identified the residues essential for coenzyme recognition. This study reveals the structural features responsible for positioning α-ketoglutarate, NADPH, ammonium ion, and the reaction intermediates in the GDH active site.

    Organizational Affiliation: 

    From the Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India pbhaumik@iitb.ac.in.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate dehydrogenaseA460Aspergillus nigerMutation(s): 0 
UniProt
Find proteins for B6V7E4 (Aspergillus niger)
Explore B6V7E4 
Go to UniProtKB:  B6V7E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6V7E4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP
Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N		 Ligand Interaction
8GL
Query on 8GL
Download Ideal Coordinates CCD File 
C [auth A](2S)-2-azanyl-2-oxidanyl-pentanedioic acid
C5 H9 N O5
GXSDWXSYZHGBBO-YFKPBYRVSA-N		 Ligand Interaction
2IT
Query on 2IT
Download Ideal Coordinates CCD File 
D [auth A](2Z)-2-iminopentanedioic acid
C5 H7 N O4
UZWLXPOZNAJCJV-UTCJRWHESA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
BB [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
AA [auth A],
AB [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
E [auth A],
EA [auth A],
F [auth A],
FA [auth A],
G [auth A],
GA [auth A],
H [auth A],
HA [auth A],
I [auth A],
IA [auth A],
J [auth A],
JA [auth A],
K [auth A],
KA [auth A],
L [auth A],
LA [auth A],
M [auth A],
MA [auth A],
N [auth A],
NA [auth A],
O [auth A],
OA [auth A],
P [auth A],
PA [auth A],
Q [auth A],
QA [auth A],
R [auth A],
RA [auth A],
S [auth A],
SA [auth A],
T [auth A],
TA [auth A],
U [auth A],
UA [auth A],
V [auth A],
VA [auth A],
W [auth A],
WA [auth A],
X [auth A],
XA [auth A],
Y [auth A],
YA [auth A],
Z [auth A],
ZA [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.41α = 90
b = 173.41β = 90
c = 241.83γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of BiotechnologyIndiaRamalingaswami Re-entry Fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Changes: Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references