1BJO

THE STRUCTURE OF PHOSPHOSERINE AMINOTRANSFERASE FROM E. COLI IN COMPLEX WITH ALPHA-METHYL-L-GLUTAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    1BJN, 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 space group P212121 using MIRAS phases in combination with density modification and was refined to an R-factor of 17 ...

    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) Immunol Res --: 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOSERINE AMINOTRANSFERASEA360Escherichia coliMutation(s): 0 
Gene Names: serC
EC: 2.6.1.52
UniProt
Find proteins for P23721 (Escherichia coli (strain K12))
Explore P23721 
Go to UniProtKB:  P23721
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOSERINE AMINOTRANSFERASEB360Escherichia coliMutation(s): 0 
Gene Names: serC
EC: 2.6.1.52
UniProt
Find proteins for P23721 (Escherichia coli (strain K12))
Explore P23721 
Go to UniProtKB:  P23721
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
GAM (Subject of Investigation/LOI)
Query on GAM

Download Ideal Coordinates CCD File 
D [auth A]ALPHA-METHYL-L-GLUTAMIC ACID
C6 H11 N O4
QHSCIWIRXWFIGH-LURJTMIESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
BL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.86α = 90
b = 94.45β = 90
c = 131.81γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MADNESSdata reduction
CCP4data scaling
SCALAdata scaling
TRUNCATEdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Other, Refinement description