PDBsum entry: 3hbl

Ligase

PDB id: 3hbl

Contents

Protein chains

1131 a.a. *

1074 a.a. *

Ligands

BTI ×4

ADP

Metals

_MN ×4

* Residue conservation analysis

PDB id:

3hbl

Name:

Ligase

Title:

Crystal structure of s. Aureus pyruvate carboxylase t908a mutant

Structure:

Pyruvate carboxylase. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Staphylococcus aureus subsp. Aureus mu50. Organism_taxid: 158878. Gene: pyca, pyruvate carboxylase, sav1114. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.71Å R-factor: 0.230 R-free: 0.279

Authors:

L.Tong,L.P.C.Yu

Key ref:

L.P.Yu et al. (2009). A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A. Structure, 17, 823-832. PubMed id: 19523900 DOI: 10.1016/j.str.2009.04.008

Date:

04-May-09 Release date: 30-Jun-09

Protein chain

Q99UY8  (Q99UY8_STAAM) -  Pyruvate carboxylase

Seq: 1150 a.a.

Struc: 1131 a.a.*

Protein chains

Q99UY8  (Q99UY8_STAAM) -  Pyruvate carboxylase

Seq: 1150 a.a.

Struc: 1074 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (2 terms)
• Biochemical function: catalytic activity (5 terms)

DOI no: 10.1016/j.str.2009.04.008

Structure 17:823-832 (2009)

PubMed id: 19523900

A symmetrical tetramer for S. aureus pyruvate carboxylase in complex with coenzyme A.

L.P.Yu, S.Xiang, G.Lasso, D.Gil, M.Valle, L.Tong.

ABSTRACT

Pyruvate carboxylase (PC) is a conserved metabolic enzyme with important cellular functions. We report crystallographic and cryo-electron microscopy (EM) studies of Staphylococcus aureus PC (SaPC) in complex with acetyl-CoA, an allosteric activator, and mutagenesis, biochemical, and structural studies of the biotin binding site of its carboxyltransferase (CT) domain. The disease-causing A610T mutation abolishes catalytic activity by blocking biotin binding to the CT active site, and Thr908 might play a catalytic role in the CT reaction. The crystal structure of SaPC in complex with CoA reveals a symmetrical tetramer, with one CoA molecule bound to each monomer, and cryo-EM studies confirm the symmetrical nature of the tetramer. These observations are in sharp contrast to the highly asymmetrical tetramer of Rhizobium etli PC in complex with ethyl-CoA. Our structural information suggests that acetyl-CoA promotes a conformation for the dimer of the biotin carboxylase domain of PC that might be catalytically more competent.

Selected figure(s)

Figure 2.
Figure 2. Structures of the A610T and T908A Mutants of SaPC
(A) Schematic drawing of the tetramer of the A610T mutant of SaPC, viewed from the top layer and colored as in Figure 1A.
(B) Molecular surface of the A610T mutant showing the steric clash between the Thr610 residue and the bound position of biotin as observed in the wild-type structure.
(C) Schematic drawing showing the overlay of the biotin binding site in the A610T mutant (in color) and the wild-type enzyme (in gray). Large conformational differences for the C-terminal segment of CT are visible, associated with the relocation of biotin to the exo site in the mutant structure. The bound position of pyruvate (in black) as observed in the wild-type SaPC structure is also shown.
(D) Schematic drawing showing the overlay of the biotin binding site in the T908A mutant (in color) and the wild-type enzyme (in gray).

Figure 5.
Figure 5. Binding Mode of CoA in SaPC
(A) SaPC displays positive cooperativity toward acetyl-CoA binding in the presence of aspartate.
(B) Detailed interactions between CoA and the BC and PT domains in the complex with SaPC. The CoA molecule is shown in black.
(C) Molecular surface of SaPC near the CoA binding site, colored as in (B).

The above figures are reprinted by permission from Cell Press: Structure (2009, 17, 823-832) copyright 2009.

Figures were selected by an automated process.