4NTM

QueD soaked with sepiapterin (selenomethionine substituted protein)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biochemical and Structural Studies of 6-Carboxy-5,6,7,8-tetrahydropterin Synthase Reveal the Molecular Basis of Catalytic Promiscuity within the Tunnel-fold Superfamily.

Miles, Z.D.Roberts, S.A.McCarty, R.M.Bandarian, V.

(2014) J.Biol.Chem. 289: 23641-23652

  • DOI: 10.1074/jbc.M114.555680
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 6-Pyruvoyltetrahydropterin synthase (PTPS) homologs in both mammals and bacteria catalyze distinct reactions using the same 7,8-dihydroneopterin triphosphate substrate. The mammalian enzyme converts 7,8-dihydroneopterin triphosphate to 6-pyruvoyltetr ...

    6-Pyruvoyltetrahydropterin synthase (PTPS) homologs in both mammals and bacteria catalyze distinct reactions using the same 7,8-dihydroneopterin triphosphate substrate. The mammalian enzyme converts 7,8-dihydroneopterin triphosphate to 6-pyruvoyltetrahydropterin, whereas the bacterial enzyme catalyzes the formation of 6-carboxy-5,6,7,8-tetrahydropterin. To understand the basis for the differential activities we determined the crystal structure of a bacterial PTPS homolog in the presence and absence of various ligands. Comparison to mammalian structures revealed that although the active sites are nearly structurally identical, the bacterial enzyme houses a His/Asp dyad that is absent from the mammalian protein. Steady state and time-resolved kinetic analysis of the reaction catalyzed by the bacterial homolog revealed that these residues are responsible for the catalytic divergence. This study demonstrates how small variations in the active site can lead to the emergence of new functions in existing protein folds.


    Organizational Affiliation

    From the Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-carboxy-5,6,7,8-tetrahydropterin synthase
A, B, C, D, E, F
121Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: queD (ygcM)
EC: 4.1.2.50
Find proteins for P65870 (Escherichia coli (strain K12))
Go to UniProtKB:  P65870
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2K8
Query on 2K8

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid
6-carboxy-5,6,7,8-tetrahydropterin
C7 H9 N5 O3
QSIYONWVWDSRRO-UWTATZPHSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.297α = 90.00
b = 111.297β = 90.00
c = 126.047γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
XDSdata reduction
REFMACrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-09-10
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Structure summary