PDBsum entry: 1hrd

Oxidoreductase

PDB-id: 1hrd

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

449 a.a. *

Waters ×521

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, hexamer
- as defined in PDB file (see also PQS)

PDB id:

1hrd

Name:

Oxidoreductase

Title:

Glutamate dehydrogenase

Structure:

Glutamate dehydrogenase. Chain: a, b, c. Ec: 1.4.1.2

Source:

Clostridium symbiosum. Organism_taxid: 1512. Strain: hb25

Biological unit:

Homo-hexamer (from PDB file)

UniProt:

Chains A, B, C: P24295 (DHE2_CLOSY)

Seq:

Struc:

Seq:

450 a.a.

Struc:

449 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.1.4.1.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

L-glutamate + H₂O + NAD⁺ = 2-oxoglutarate + NH₃ + NADH (see diagram below)

Resolution:

1.96Å

R-factor:

0.172

Authors:

K.L.Britton,P.J.Baker,T.J.Stillman,D.W.Rice

Key ref:

K.S.Yip et al. (1995). The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.. Structure, 3, 1147-1158. [PubMed id: 8591026] [DOI: 10.1016/S0969-2126(01)00251-9]

Date:

03-Apr-96

Release date:

12-Mar-97

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1016/S0969-2126(01)00251-9

Structure 3:1147-1158 (1995)

PubMed id: 8591026

The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.

K.S.Yip, T.J.Stillman, K.L.Britton, P.J.Artymiuk, P.J.Baker, S.E.Sedelnikova, P.C.Engel, A.Pasquo, R.Chiaraluce, V.Consalvi.

ABSTRACT

BACKGROUND: The hyperthermophile Pyrococcus furiosus is one of the most thermostable organisms known, with an optimum growth temperature of 100 degrees C. The proteins from this organism display extreme thermostability. We have undertaken the structure determination of glutamate dehydrogenase from P. furiosus in order to gain further insights into the relationship between molecular structure and thermal stability. RESULTS: The structure of P. furiosus glutamate dehydrogenase, a homohexameric enzyme, has been determined at 2.2 A resolution and compared with the structure of glutamate dehydrogenase from the mesophile Clostridium symbiosum. CONCLUSIONS: Comparison of the structures of these two enzymes has revealed one major difference: the structure of the hyperthermophilic enzyme contains a striking series of ion-pair networks on the surface of the protein subunits and buried at both interdomain and intersubunit interfaces. We propose that the formation of such extended networks may represent a major stabilizing feature associated with the adaptation of enzymes to extreme temperatures.

Selected figure(s)

Figure 3.
Figure 3. Superpositions of Cs (blue) and Pf (green) GluDHs. (a) The N-terminal regions (α1–α5 in Cs, α1–α2 in Pf) are shown. Helices α2 (Cs) and α1 (Pf) superimpose well as do helices α5 (Cs) and α2 (Pf). However, α1 (Cs) is completely absent in Pf and the loop α1–α2 in Pf is much shorter, replacing α3 and α4 in Cs. (b) Superposition of the region βh–βj which, in both GluDHs, forms the recognition site for the adenine ribose moiety. Figure 3. Superpositions of Cs (blue) and Pf (green) GluDHs. (a) The N-terminal regions (α1–α5 in Cs, α1–α2 in Pf) are shown. Helices α2 (Cs) and α1 (Pf) superimpose well as do helices α5 (Cs) and α2 (Pf). However, α1 (Cs) is completely absent in Pf and the loop α1–α2 in Pf is much shorter, replacing α3 and α4 in Cs. (b) Superposition of the region βh–βj which, in both GluDHs, forms the recognition site for the adenine ribose moiety. (Figure prepared using MIDASPLUS [[4]57 and [5]58].)

Figure 5.
Figure 5. The cluster of isoleucine residues in the core of domain I in the Pf GluDH structure. Figure 5. The cluster of isoleucine residues in the core of domain I in the Pf GluDH structure. (Drawn with MIDASPLUS [[3]57 and [4]58].)

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1147-1158) copyright 1995.

Figures were selected by an automated process.