PDBsum entry: 2dc1

Oxidoreductase

PDB id: 2dc1

Contents

Protein chains

236 a.a. *

Ligands

CIT ×2

NAD ×2

Waters ×136

* Residue conservation analysis

PDB id:

2dc1

Name:

Oxidoreductase

Title:

Crystal structure of l-aspartate dehydrogenase from hyperthermophilic archaeon archaeoglobus fulgidus

Structure:

L-aspartate dehydrogenase. Chain: a, b. Engineered: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.217 R-free: 0.226

Authors:

K.Yoneda,H.Sakuraba,H.Tsuge,T.Ohshima

Key ref:

K.Yoneda et al. (2007). Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex. Febs J, 274, 4315-4325. PubMed id: 17651440 DOI: 10.1111/j.1742-4658.2007.05961.x

Date:

19-Dec-05 Release date: 26-Dec-06

Protein chains

O28440  (ASPD_ARCFU) -  Probable L-aspartate dehydrogenase

Seq: 236 a.a.

Struc: 236 a.a.

Enzyme reactions

• Enzyme class: E.C.1.4.1.21 - Aspartate dehydrogenase.
• Reaction: L-aspartate + H₂O + NAD(P)(+) = oxaloacetate + NH₃ + NAD(P)H

L-aspartate + H(2)O + NAD(P)(+) (Bound ligand (Het Group name = NAD) matches with 91.00% similarity) = oxaloacetate (Bound ligand (Het Group name = CIT) matches with 69.00% similarity) + NH(3) + 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 (4 terms)
• Biochemical function: nucleotide binding (4 terms)

reference

DOI no: 10.1111/j.1742-4658.2007.05961.x

Febs J 274:4315-4325 (2007)

PubMed id: 17651440

Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex.

K.Yoneda, H.Sakuraba, H.Tsuge, N.Katunuma, T.Ohshima.

ABSTRACT

The crystal structure of the highly thermostable L-aspartate dehydrogenase (L-aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidus L-aspDH was refined at a resolution of 1.9 A with a crystallographic R-factor of 21.7% (R(free) = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidus L-aspDH/NAD/citrate ternary complex and the Thermotoga maritima L-aspDH/NAD binary complex showed that A. fulgidus L-aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritima L-aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidus L-aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two L-aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to L-aspDH and of the molecular basis of the high thermostability of a hyperthermophilic L-aspDH.