PDBsum entry 3c20

Transferase

PDB id: 3c20

Contents

Protein chains

465 a.a. *

Ligands

ASP ×2

FMT ×2

Waters ×13

* Residue conservation analysis

PDB id:

3c20

Name:

Transferase

Title:

Crystal structure of threonine-sensitive aspartokinase from methanococcus jannaschii with l-aspartate

Structure:

Probable aspartokinase. Chain: a, b. Synonym: aspartate kinase. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: mj0571. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.240 R-free: 0.273

Authors:

X.Liu,A.G.Pavlovsky,R.E.Viola

Key ref:

X.Liu et al. (2008). The structural basis for allosteric inhibition of a threonine-sensitive aspartokinase. J Biol Chem, 283, 16216-16225. PubMed id: 18334478 DOI: 10.1074/jbc.M800760200

Date:

24-Jan-08 Release date: 29-Apr-08

Protein chains

Q57991  (AK_METJA) -  Probable aspartokinase from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 473 a.a.

Struc: 465 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.2.4 - aspartate kinase.
• Pathway: Lysine biosynthesis (early stages)
• Reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP

L-aspartate + ATP (Bound ligand (Het Group name = ASP) corresponds exactly) = 4-phospho-L-aspartate + ADP

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

reference

DOI no: 10.1074/jbc.M800760200

J Biol Chem 283:16216-16225 (2008)

PubMed id: 18334478

The structural basis for allosteric inhibition of a threonine-sensitive aspartokinase.

X.Liu, A.G.Pavlovsky, R.E.Viola.

ABSTRACT

The commitment step to the aspartate pathway of amino acid biosynthesis is the phosphorylation of aspartic acid catalyzed by aspartokinase (AK). Most microorganisms and plants have multiple forms of this enzyme, and many of these isofunctional enzymes are subject to feedback regulation by the end products of the pathway. However, the archeal species Methanococcus jannaschii has only a single, monofunctional form of AK. The substrate l-aspartate binds to this recombinant enzyme in two different orientations, providing the first structural evidence supporting the relaxed regiospecificity previously observed with several alternative substrates of Escherichia coli AK ( Angeles, T. S., Hunsley, J. R., and Viola, R. E. (1992) Biochemistry 31, 799-805 ). Binding of the nucleotide substrate triggers significant domain movements that result in a more compact quaternary structure. In contrast, the highly cooperative binding of the allosteric regulator l-threonine to multiple sites on this dimer of dimers leads to an open enzyme structure. A comparison of these structures supports a mechanism for allosteric regulation in which the domain movements induced by threonine binding causes displacement of the substrates from the enzyme, resulting in a relaxed, inactive conformation.

Selected figure(s)

Figure 3.
FIGURE 3. Nucleotide-induced domain closure in mjAK. A, an overlay of the ternary complex (yellow ribbons) on the binary complex (blue ribbons) shows that binding of the ATP analog AMP-PNP induces a 12.5° rotation around the hinge bending region (green) of the regulatory domain (light blue) toward the kinase domain (dark blue). B, an expansion of the active site showing the movement of latch loop I into position to form binding interactions with the ribose ring of AMP-PNP and the closing of latch loop II to complete the hydrophobic pocket of adenine ring binding.

Figure 4.
FIGURE 4. The mjAK/L-threonine structure reveals two sets of threonine binding sites. Each L-threonine is positioned in the binding site by interactions between its functional groups and the enzyme. Inset A, the binding modes of two threonines at the A-B dimer interface site. This inset is rotated by 90° to provide a clearer view of the two bound threonines. Inset B, the binding of a single threonine with lower occupancy at the C-D dimer interface site. This inset is rotated by 180° to show the binding interactions at this site. Inset C, representative binding of threonine at the weaker secondary sites in each monomer, located adjacent to the active site.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 16216-16225) copyright 2008.

Figures were selected by an automated process.