PDBsum entry: 1hwy

Oxidoreductase

PDB id: 1hwy

Contents

Protein chains

(+ 0 more) 501 a.a. *

Ligands

PO4 ×24

AKG ×6

NAD ×12

Waters ×36

* Residue conservation analysis

PDB id:

1hwy

Name:

Oxidoreductase

Title:

Bovine glutamate dehydrogenase complexed with NAD and 2-oxog

Structure:

Glutamate dehydrogenase. Chain: a, b, c, d, e, f. Synonym: gdh. Ec: 1.4.1.3

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: liver. Organelle: mitochondria. Cellular_location: inner mitochondrial matrix

Biol. unit:

Hexamer (from PQS)

Resolution:

3.20Å R-factor: 0.230 R-free: 0.290

Authors:

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

Key ref:

T.J.Smith et al. (2001). Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J Mol Biol, 307, 707-720. PubMed id: 11254391 DOI: 10.1006/jmbi.2001.4499

Date:

10-Jan-01 Release date: 31-Jan-01

Protein chains

P00366  (DHE3_BOVIN) -  Glutamate dehydrogenase 1, mitochondrial

Seq: 558 a.a.

Struc: 501 a.a.*

* PDB and UniProt seqs differ at 17 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.4.1.3 - Glutamate dehydrogenase (NAD(P)(+)).
• Reaction: L-glutamate + H₂O + NAD(P)(+) = 2-oxoglutarate + NH₃ + NAD(P)H

L-glutamate + H(2)O + NAD(P)(+) (Bound ligand (Het Group name = NAD) matches with 91.67% similarity) = 2-oxoglutarate (Bound ligand (Het Group name = AKG) corresponds exactly) + NH(3) + NAD(P)H

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: mitochondrion (3 terms)
• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: binding (8 terms)

reference

DOI no: 10.1006/jmbi.2001.4499

J Mol Biol 307:707-720 (2001)

PubMed id: 11254391

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

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

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. 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.

Selected figure(s)

Figure 3.
Figure 3. Refined structure of the bound GTP molecule in the NADH delta GLU delta GTP complex. (a) Schematic of the bound GTP mol- ecule and its contact with the enzyme at the base of the antenna. The view here is approximately from the antenna towards the NAD binding domain. Note the contacts between the purine ring and E292 and K289. (b) 6-Fold averaged omit map of the bound GTP.

Figure 5.
Figure 5. Structure of the active site ligands in the NAD+ delta a-KG complex. (a) Schematic diagram of the NAD+ and a-KG molecules bound in the active site. The orien- tation is the same as that used in Figure 2. (b) 6-Fold averaged, omit electron density of the bound ligands (black lines) with their atomic models included.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 707-720) copyright 2001.

Figures were selected by an automated process.