PDBsum entry 1w3u

Transferase

PDB id: 1w3u

Contents

Protein chain

360 a.a. *

Ligands

PLP

GOL

Waters ×340

* Residue conservation analysis

PDB id:

1w3u

Name:

Transferase

Title:

Crystal structure of phosphoserine aminotransferase from bacillus circulans var. Alkalophilus

Structure:

Phosphoserine aminotransferase. Chain: a. Synonym: phosphohydroxythreonine aminotransferase, psat. Engineered: yes. Mutation: yes. Other_details: schiff base link between a 197 and a 363

Source:

Bacillus circulans. Organism_taxid: 1397. Variant: alkalophilus. Atcc: 21783. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.50Å R-factor: 0.144 R-free: 0.208

Authors:

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

Key ref:

A.P.Dubnovitsky et al. (2005). Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus. Protein Sci, 14, 97. PubMed id: 15608117 DOI: 10.1110/ps.041029805

Date:

20-Jul-04 Release date: 22-Dec-04

Protein chain

Q59196  (SERC_NIACI) -  Phosphoserine aminotransferase from Niallia circulans

Seq: 362 a.a.

Struc: 360 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

O-phospho-L-serine (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate

4-(phosphooxy)-L-threonine (Bound ligand (Het Group name = GOL) matches with 45.45% similarity) + 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: 10.1110/ps.041029805

Protein Sci 14:97 (2005)

PubMed id: 15608117

Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus.

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

ABSTRACT

The crystal structure of the vitamin B(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile Bacillus alcalophilus has been determined at 1.08 A resolution. The model was refined to an R-factor of 11.7% (R(free) = 13.9%). The enzyme displays a narrow pH optimum of enzymatic activity at pH 9.0. The final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from Escherichia coli and to that of phosphoserine aminotransferase from a facultative alkaliphile, Bacillus circulans subsp. alkalophilus. All three enzymes are homodimers with each monomer comprising a two-domain architecture. Despite the high structural similarity, the alkaliphilic representatives possess a set of distinctive structural features. Two residues directly interacting with pyridoxal-5'-phosphate are replaced, and an additional hydrogen bond to the O3' atom of the cofactor is present in alkaliphilic phosphoserine aminotransferases. The number of hydrogen bonds and hydrophobic interactions at the dimer interface is increased. Hydrophobic interactions between the two domains in the monomers are enhanced. Moreover, the number of negatively charged amino acid residues increases on the solvent-accessible molecular surface and fewer hydrophobic residues are exposed to the solvent. Further, the total amount of ion pairs and ion networks is significantly reduced in the Bacillus enzymes, while the total number of hydrogen bonds is increased. The mesophilic enzyme from Escherichia coli contains two additional beta-strands in a surface loop with a third beta-strand being shorter in the structure. The identified structural features are proposed to be possible factors implicated in the alkaline adaptation of phosphoserine aminotransferase.

Selected figure(s)

Figure 3.
Figure 3. Ribbon representation of the BALC PSAT dimer. The two monomers are depicted in yellow and in blue, respectively. Ligands included in the final model (PLP, PEG, HEPES, glycerol) are shown in ball-and-sticks. Mg2+ ions are shown as gray spheres and Cl- ions as pink spheres. (A) View along the twofold noncrystallographic axis. The active site clefts are shown with arrows. (B) BALC PSAT dimer after 90° rotation. The twofold axis in this orientation is vertical and lying within the plane of the figure. The figure was produced using MOLSCRIPT (Kraulis 1991) and Raster3D (Merritt and Murphy 1994).

Figure 5.
Figure 5. Definition of torsion angle for the internal aldimine bond and atom names in pyridoxal-5'-phosphate. The figure was produced using ISIS/Draw (MDL, Inc.).

The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 97-0) copyright 2005.

Figures were selected by an automated process.