4FIR

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.

Matsuura, A.Yoon, J.Y.Yoon, H.J.Lee, H.H.Suh, S.W.

(2012) Mol.Cells 34: 407-412

  • DOI: 10.1007/s10059-012-0198-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B(6) and is de novo synthesized from three substrates, dihydroxyacetone phosphate (DHAP), riburose 5-phosphate (RBP), and ammonia hydrolysed from glutamine. Glutamine amidotransf ...

    Pyridoxal 5'-phosphate (PLP) is the biologically active form of vitamin B(6) and is de novo synthesized from three substrates, dihydroxyacetone phosphate (DHAP), riburose 5-phosphate (RBP), and ammonia hydrolysed from glutamine. Glutamine amidotransferase (PdxT) catalyzes the production of ammonia from glutamine, while PdxS catalyzes the following condensation of ribulose 5-phosphate (Ru5P), glyceraldehyde-3-phosphate (G3P), and ammonia. PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins, but its structure and function are unknown. To provide further structural information on the role of the insertion region, the oligomeric state, and ligand binding mode of P. horikoshii PdxS, the crystal structure of PdxS from P. horikoshii was solved in two forms: (i) apo form, (ii) r ibose 5-phosphate (R5P) complex and the quaternary structure of PdxS in solution was determined by analytical gel filtration. P. horikoshii PdxS forms hexamer in solution based on analytical gel filtration data. When we superimpose the structure of P. horikoshii PdxS with other dodecamer structures of PdxS, the additional insertion is located apart from the active site and induces a steric clash on the hexamer-hexamer interface of PdxS proteins. Our results suggest that the additional insertion perturbs dodecamer formation of P. horikoshii PdxS.


    Organizational Affiliation

    Department of Bio & Nano Chemistry, Kookmin University, Seoul 136-702, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyridoxal biosynthesis lyase pdxS
A, B, C, D, E, F
335Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
Gene Names: pdxS
EC: 4.3.3.6
Find proteins for O59080 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59080
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R5P
Query on R5P

Download SDF File 
Download CCD File 
A, B, C, D, E, F
RIBOSE-5-PHOSPHATE
C5 H11 O8 P
PPQRONHOSHZGFQ-LMVFSUKVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.165α = 90.00
b = 179.065β = 102.53
c = 109.359γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
CNSphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release