PDBsum entry 1bjo

Aminotransferase

PDB id: 1bjo

Contents

Protein chains

360 a.a. *

Ligands

PLP-GAM

Waters ×50

* Residue conservation analysis

PDB id:

1bjo

Name:

Aminotransferase

Title:

The structure of phosphoserine aminotransferase from e. Coli in complex with alpha-methyl-l-glutamate

Structure:

Phosphoserine aminotransferase. Chain: a. Synonym: psat. Engineered: yes. Other_details: in chain a an external aldimine intermediate between pyridoxal-5'-phosphate and alpha-methyl-l-glutamate is non-covalently bound while in chain b a pyridoxal-5'-phosphate molecule is covalently bound in an aldimine linkage to a lysine side chain. Phosphoserine aminotransferase.

Source:

Escherichia coli. Organism_taxid: 562. Gene: serc. Gene: serc

Biol. unit:

Dimer (from PDB file)

Resolution:

2.80Å R-factor: 0.185 R-free: 0.251

Authors:

G.Hester,W.Stark,J.N.Jansonius

Key ref:

G.Hester et al. (1999). Crystal structure of phosphoserine aminotransferase from Escherichia coli at 2.3 A resolution: comparison of the unligated enzyme and a complex with alpha-methyl-l-glutamate. J Mol Biol, 286, 829-850. PubMed id: 10024454 DOI: 10.1006/jmbi.1998.2506

Date:

25-Jun-98 Release date: 04-Nov-98

Protein chains

P23721  (SERC_ECOLI) -  Phosphoserine aminotransferase from Escherichia coli (strain K12)

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 + 2-oxoglutarate = 3-phosphooxypyruvate + L-glutamate (Bound ligand (Het Group name = GAM) matches with 90.91% similarity)

4-(phosphooxy)-L-threonine + 2-oxoglutarate = (R)-3-hydroxy-2-oxo-4- phosphooxybutanoate + L-glutamate (Bound ligand (Het Group name = GAM) matches with 90.91% similarity)

• 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: 10.1006/jmbi.1998.2506

J Mol Biol 286:829-850 (1999)

PubMed id: 10024454

Crystal structure of phosphoserine aminotransferase from Escherichia coli at 2.3 A resolution: comparison of the unligated enzyme and a complex with alpha-methyl-l-glutamate.

G.Hester, W.Stark, M.Moser, J.Kallen, Z.Marković-Housley, J.N.Jansonius.

ABSTRACT

Phosphoserine aminotransferase (PSAT; EC 2.6.1.52), a member of subgroup IV of the aminotransferases, catalyses the conversion of 3-phosphohydroxypyruvate to l-phosphoserine. The crystal structure of PSAT from Escherichia coli has been solved in space group P212121 using MIRAS phases in combination with density modification and was refined to an R-factor of 17.5% (Rfree=20.1 %) at 2.3 A resolution. In addition, the structure of PSAT in complex with alpha-methyl-l-glutamate (AMG) has been refined to an R-factor of 18.5% (Rfree=25.1%) at 2.8 A resolution. Each subunit (361 residues) of the PSAT homodimer is composed of a large pyridoxal-5'-phosphate binding domain (residues 16-268), consisting of a seven-stranded mainly parallel beta-sheet, two additional beta-strands and seven alpha-helices, and a small C-terminal domain, which incorporates a five-stranded beta-sheet and two alpha-helices. A three-dimensional structural comparison to four other vitamin B6-dependent enzymes reveals that three alpha-helices of the large domain, as well as an N-terminal domain (subgroup II) or subdomain (subgroup I) are absent in PSAT. Its only 15 N-terminal residues form a single beta-strand, which participates in the beta-sheet of the C-terminal domain. The cofactor is bound through an aldimine linkage to Lys198 in the active site. In the PSAT-AMG complex Ser9 and Arg335 bind the AMG alpha-carboxylate group while His41, Arg42 and His328 are involved in binding the AMG side-chain. Arg77 binds the AMG side-chain indirectly through a solvent molecule and is expected to position itself during catalysis between the PLP phosphate group and the substrate side-chain. Comparison of the active sites of PSAT and aspartate aminotransferase suggests a similar catalytic mechanism, except for the transaldimination step, since in PSAT the Schiff base is protonated. Correlation of the PSAT crystal structure to a published profile sequence analysis of all subgroup IV members allows active site modelling of nifs and the proposal of a likely molecular reaction mechanism.

Selected figure(s)

Figure 1.
Figure 1. Nomenclature of atoms for PLP-Lys198 aldimine and for the external aldimine with AMG.

Figure 5.
Figure 5. Comparison of structure topologies by superpositions of C^α traces of PSAT with those of DGD and E. coli AAT, respectively, using DALI algorithm [Holm and Sander 1993]. In both stereo diagrams PSAT is displayed in fat lines while the superimposed molecule is displayed in thin lines. N and C termini are labelled. (a) Stereo diagram of superimposed C^α traces of closed form of AAT and PSAT-AMG complex. (b) Stereo diagram of superimposed C^α traces of DGD and native PSAT. Pictures generated using program BOBSCRIPT [Kraulis 1991 and Esnouf 1998]. Program RASTER3D was used additionally to generate (b) [Bacon and Anderson 1988 and Merrit and Murphy 1994].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 286, 829-850) copyright 1999.

Figures were selected by an automated process.