PDBsum entry: 1euz

Oxidoreductase

PDB id: 1euz

Contents

Protein chains

(+ 0 more) 416 a.a. *

Ligands

SO4 ×17

* Residue conservation analysis

PDB id:

1euz

Name:

Oxidoreductase

Title:

Glutamate dehydrogenase from thermococcus profundus in the u state

Structure:

Glutamate dehydrogenase. Chain: a, b, c, d, e, f. Synonym: gludh. Engineered: yes

Source:

Thermococcus profundus. Organism_taxid: 49899. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PQS)

Resolution:

2.25Å R-factor: 0.187 R-free: 0.250

Authors:

M.Nakasako

Key ref:

M.Nakasako et al. (2001). Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering. Biochemistry, 40, 3069-3079. PubMed id: 11258921 DOI: 10.1021/bi002482x

Date:

19-Apr-00 Release date: 25-Apr-01

Protein chains

O74024  (DHE3_THEPR) -  Glutamate dehydrogenase

Seq: 419 a.a.

Struc: 416 a.a.

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

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

 Gene Ontology (GO) functional annotation 

• Biological process: oxidation-reduction process (2 terms)
• Biochemical function: nucleotide binding (4 terms)

reference

DOI no: 10.1021/bi002482x

Biochemistry 40:3069-3079 (2001)

PubMed id: 11258921

Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering.

M.Nakasako, T.Fujisawa, S.Adachi, T.Kudo, S.Higuchi.

ABSTRACT

Here we describe the large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase. Glutamate dehydrogenase from Thermococcus profundus is composed of six identical subunits of M(r) 46K, each with two distinct domains of roughly equal size separated by a large active-site cleft. The enzyme in the unligated state was crystallized so that one hexamer occupied a crystallographic asymmetric unit, and the crystal structure of the hexamer was solved and refined at a resolution of 2.25 A with a crystallographic R-factor of 0.190. In that structure, the six subunits displayed significant conformational variations with respect to the orientations of the two domains. The variation was most likely explained as a hinge-bending motion caused by small changes in the main chain torsion angle of the residue composing a loop connecting the two domains. Small-angle X-ray scattering profiles both at 293 and 338 K suggested that the apparent molecular size of the hexamer was slightly larger in solution than in the crystalline state. These results led us to the conclusion that (i) the spontaneous domain motion was the property of the enzyme in solution, (ii) the domain motion was trapped in the crystallization process through different modes of crystal contacts, and (iii) the magnitude of the motion in solution was greater than that observed in the crystal structure. The present cryogenic diffraction experiment enabled us to identify 1931 hydration water molecules around the hexamer. The hydration structures around the subunits exhibited significant changes in accord with the degree of the domain movement. In particular, the hydration water molecules in the active-site cleft were rearranged markedly through migrations between specific hydration sites in coupling strongly with the domain movement. We discussed the cooperative dynamics between the domain motion and the hydration structure changes in the active site of the enzyme. The present study provides the first example of a visualized hydration structure varying transiently with the dynamic movements of enzymes and may form a new concept of the dynamics of multidomain enzymes in solution.