PDBsum entry 2c0r

Transferase

PDB id: 2c0r

Contents

Protein chains

361 a.a. *

Ligands

PLP ×2

Waters ×809

* Residue conservation analysis

PDB id:

2c0r

Name:

Transferase

Title:

Crystal structure of phosphoserine aminotransferase from bacillus circulans var. Alkalophilus at ph 8.5

Structure:

Phosphoserine aminotransferase. Chain: a, b. Synonym: psat. Engineered: yes. Mutation: yes

Source:

Bacillus circulans. Organism_taxid: 1397. Variant: alkalophilus. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.20Å R-factor: 0.154 R-free: 0.212

Authors:

E.G.Kapetaniou,A.C.Papageorgiou

Key ref:

E.G.Kapetaniou et al. (2006). Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: thermodynamic and crystallographic studies. Proteins, 63, 742-753. PubMed id: 16532449 DOI: 10.1002/prot.20935

Date:

07-Sep-05 Release date: 22-Mar-06

Protein chains

Q59196  (SERC_NIACI) -  Phosphoserine aminotransferase from Niallia circulans

Seq: 362 a.a.

Struc: 361 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.6.1.52 - phosphoserine transaminase.
• Reaction:
  1. O-phospho-L-serine + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate
  2. 4-(phosphooxy)-L-threonine + 2-oxoglutarate = (R)-3-hydroxy-2-oxo-4- phosphooxybutanoate + L-glutamate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1002/prot.20935

Proteins 63:742-753 (2006)

PubMed id: 16532449

Effect of pH on the structure and stability of Bacillus circulans ssp. alkalophilus phosphoserine aminotransferase: thermodynamic and crystallographic studies.

E.G.Kapetaniou, A.Thanassoulas, A.P.Dubnovitsky, G.Nounesis, A.C.Papageorgiou.

ABSTRACT

pH is one of the key parameters that affect the stability and function of proteins. We have studied the effect of pH on the pyridoxal-5'-phosphate-dependent enzyme phosphoserine aminotransferase produced by the facultative alkaliphile Bacillus circulans ssp. alkalophilus using thermodynamic and crystallographic analysis. Enzymatic activity assay showed that the enzyme has maximum activity at pH 9.0 and relative activity less than 10% at pH 7.0. Differential scanning calorimetry and circular dichroism experiments revealed variations in the stability and denaturation profiles of the enzyme at different pHs. Most importantly, release of pyridoxal-5'-phosphate and protein thermal denaturation were found to occur simultaneously at pH 6.0 in contrast to pH 8.5 where denaturation preceded cofactor's release by approximately 3 degrees C. To correlate the observed differences in thermal denaturation with structural features, the crystal structure of phosphoserine aminotransferase was determined at 1.2 and 1.5 A resolution at two different pHs (8.5 and 4.6, respectively). Analysis of the two structures revealed changes in the vicinity of the active site and in surface residues. A conformational change in a loop involved in substrate binding at the entrance of the active site has been identified upon pH change. Moreover, the number of intramolecular ion pairs was found reduced in the pH 4.6 structure. Taken together, the presented kinetics, thermal denaturation, and crystallographic data demonstrate a potential role of the active site in unfolding and suggest that subtle but structurally significant conformational rearrangements are involved in the stability and integrity of phosphoserine aminotransferase in response to pH changes.

Selected figure(s)

Figure 1.
Figure 1. Schematic representation of the chemical reaction catalyzed by phosphoserine aminotransferase.

Figure 7.
Figure 7. Ribbon representation of the BCIR PSAT structure at pH 8.5 (A) dimer (B) monomer. Secondary-structure elements were calculated using DSSP.[29] The -helices are shown in yellow and the -strands in cyan. N- and C-termini are shown as spheres and PLP molecules in space filling (A) and ball-and-stick (B). The small domain contains an extended five-stranded -sheet, composed of a two-stranded parallel -sheet ( 1 and 13) and a three-stranded antiparallel -sheet (+ 11, - 12, - 14). The large domain contains the conservative among PLP-dependent enzymes[44] seven-stranded -sheet ( 2- 5 and 7- 9) with all -strands parallel except 9. Two additional -strands ( 6 and 10), six -helices ( 1- 6), and six 3[10]-helices complete the large domain. Helix 7 connects the large domain with the small domain. The five-stranded -sheet is flanked by helix 7 and two additional helices ( 8 and 9) close to the C-terminus.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 742-753) copyright 2006.

Figures were selected by an automated process.