6DHD

Bovine glutamate dehydrogenase complexed with NADH, GTP, glutamate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


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Literature

Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.

Smith, T.J., Peterson, P.E., Schmidt, T., Fang, J., Stanley, C.A.

(2001) J Mol Biol 307: 707-720

  • DOI: 10.1006/jmbi.2001.4499
  • Primary Citation of Related Structures:  
    6DHQ, 6DHD, 1HWY

  • PubMed Abstract: 

    • Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules ...

    Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules. The major allosteric inhibitors are GTP and NADH and the two main allosteric activators are ADP and NAD(+). The structures presented here have refined and modified the previous structural model of allosteric regulation inferred from the original boGDH.NADH.GLU.GTP complex. The boGDH.NAD(+).alpha-KG complex structure clearly demonstrates that the second coenzyme-binding site lies directly under the "pivot helix" of the NAD(+) binding domain. In this complex, phosphates are observed to occupy the inhibitory GTP site and may be responsible for the previously observed structural stabilization by polyanions. The boGDH.NADPH.GLU.GTP complex shows the location of the additional phosphate on the active site coenzyme molecule and the GTP molecule bound to the GTP inhibitory site. As expected, since NADPH does not bind well to the second coenzyme site, no evidence of a bound molecule is observed at the second coenzyme site under the pivot helix. Therefore, these results suggest that the inhibitory GTP site is as previously identified. However, ADP, NAD(+), and NADH all bind under the pivot helix, but a second GTP molecule does not. Kinetic analysis of a hyperinsulinism/hyperammonemia mutant strongly suggests that ATP can inhibit the reaction by binding to the GTP site. Finally, the fact that NADH, NAD(+), and ADP all bind to the same site requires a re-analysis of the previous models for NADH inhibition.

    Organizational Affiliation: 

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA. tom@bragg.bio.purdue.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate dehydrogenase 1, mitochondrialA, B, C, D, E, F501Bos taurusMutation(s): 0 
Gene Names: GLUD1, GLUD
EC: 1.4.1.2 (PDB Primary Data), 1.4.1.3 (UniProt)
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI
Download Ideal Coordinates CCD File 
BA [auth F] , CA [auth F] , H [auth A] , I [auth A] , L [auth B] , N [auth B] , Q [auth C] , R [auth C] , 
BA [auth F],  CA [auth F],  H [auth A],  I [auth A],  L [auth B],  N [auth B],  Q [auth C],  R [auth C],  T [auth D],  U [auth D],  X [auth E],  Y [auth E]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N		 Ligand Interaction
GTP (Subject of Investigation/LOI)
Query on GTP
Download Ideal Coordinates CCD File 
 DA [auth F], J [auth A], M [auth B], P [auth C], V [auth D], Z [auth E]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GLU
Query on GLU
Download Ideal Coordinates CCD File 
 AA [auth F], G [auth A], K [auth B], O [auth C], S [auth D], W [auth E]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124α = 90
b = 102.5β = 101.64
c = 167.302γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2018-05-19 
  • Released Date: 2018-07-25 
    • Deposition Author(s): Smith, T.J.
  • This entry supersedes: 3MW9

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release