1BJN

STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.

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

(1999) J.Mol.Biol. 286: 829-850

  • DOI: 10.1006/jmbi.1998.2506
  • Primary Citation of Related Structures:  1BJO

  • PubMed 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 spac ...

    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.


    Related Citations: 
    • The Three Dimensional Structure of Phosphoserine Aminotransferase from Escherichia Coli
      Stark, W.,Kallen, J.,Markovic-Housley, Z.,Fol, B.,Kania, M.,Jansonius, J.N.
      (1991) Enzymes Dependent on Pyridoxal Phosphate and Other Carbonyl Compounds as Cofactors: Proceedings of the 8Th International Symposium on Vitamin B6 and Carbonyl Catalysis --: 111
    • Crystallographic and Solution Studies on Phosphoserine Aminotransferase (Psat) from E. Coli
      Kallen, J.,Kania, M.,Markovic-Housley, Z.,Vincent, M.G.,Jansonius, J.N.
      (1987) Biochemistry of Vitamin B6: Proceedings of the 7Th International Congress on Chemical and Biological Aspects of Vitamin B6 Catalysis (in: Iub Symp. Ser., V.166) --: 157


    Organizational Affiliation

    Biozentrum, University of Basel, Klingelbergstrasse 70, Basel, CH-4056, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOSERINE AMINOTRANSFERASE
A, B
360Escherichia coli (strain K12)Gene Names: serC (pdxC, pdxF)
EC: 2.6.1.52
Find proteins for P23721 (Escherichia coli (strain K12))
Go to UniProtKB:  P23721
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A, B
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.740α = 90.00
b = 94.740β = 90.00
c = 133.640γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance