PDBsum entry 1j3b

Transferase

PDB id: 1j3b

Contents

Protein chains

513 a.a. *

Ligands

PO4 ×9

GOL ×2

Metals

_CA ×2

Waters ×709

* Residue conservation analysis

PDB id:

1j3b

Name:

Transferase

Title:

Crystal structure of atp-dependent phosphoenolpyruvate carboxykinase from thermus thermophilus hb8

Structure:

Atp-dependent phosphoenolpyruvate carboxykinase. Chain: a, b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.207 R-free: 0.226

Authors:

M.Sugahara,M.Miyano,N.Kunishima,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

M.Sugahara et al. (2005). Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability. Acta Crystallogr D Biol Crystallogr, 61, 1500-1507. PubMed id: 16239727 DOI: 10.1107/S090744490502651X

Date:

21-Jan-03 Release date: 11-Feb-03

Protein chains

Q5SLL5  (PCKA_THET8) -  Phosphoenolpyruvate carboxykinase (ATP) from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 529 a.a.

Struc: 513 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.49 - phosphoenolpyruvate carboxykinase (ATP).
• Reaction: oxaloacetate + ATP = phosphoenolpyruvate + ADP + CO2

oxaloacetate + ATP (Bound ligand (Het Group name = GOL) matches with 50.00% similarity) = phosphoenolpyruvate + ADP + CO2 (Bound ligand (Het Group name = PO4) matches with 50.00% similarity)

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

reference

DOI no: 10.1107/S090744490502651X

Acta Crystallogr D Biol Crystallogr 61:1500-1507 (2005)

PubMed id: 16239727

Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.

M.Sugahara, N.Ohshima, Y.Ukita, M.Sugahara, N.Kunishima.

ABSTRACT

In order to understand the induced fit and the thermostabilization mechanisms of ATP-dependent phosphoenolpyruvate carboxykinase, the crystal structure of the enzyme from the extreme thermophile Thermus thermophilus HB8 (TtPEPCK) was determined and compared with those of orthologues of known structure from two mesophilic organisms. The protomer structures in these orthologues, which exhibit open/closed interdomain conformations, are similar. Isomorphous crystals of unliganded and ATP-bound TtPEPCK were obtained. The asymmetric units of both crystal forms contain two protomers A and B with closed and open conformations, respectively. ATP was only observed in the interdomain cleft of the closed protomer, suggesting that the induced fit of TtPEPCK agrees with the so-called ;conformational selection' mechanism where ligand binding is not essential for domain closure although its binding leads to the stabilization of the closed state. A bound calcium observed in the N-terminal domain of TtPEPCK probably contributes to the thermal stability. A combination of hydrophobic effects, ion pairs and entropic effects might also contribute to the thermostability of TtPEPCK.

Selected figure(s)

Figure 1.
Figure 1 Ribbon diagram of the crystal structure of TtPEPCK. The asymmetric unit of the ATP-liganded form comprising the A chain with closed conformation (blue and light blue) and the B chain with open conformation (red and pink) is shown. The N- and C-terminal domains are distinguished by dark and light colours, respectively. Bound calcium ions are depicted as green spheres. ATP, phosphate ions and glycerol molecules are depicted as stick models.

Figure 4.
Figure 4 Stereo representation of the calcium-binding site. Bound calcium and water are depicted as green and red spheres, respectively.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 1500-1507) copyright 2005.

Figures were selected by an automated process.