1BS1

DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.

Kack, H.Sandmark, J.Gibson, K.J.Schneider, G.Lindqvist, Y.

(1998) Protein Sci. 7: 2560-2566

  • DOI: 10.1002/pro.5560071209
  • Primary Citation of Related Structures:  1DAM

  • PubMed Abstract: 
  • The crystal structures of two complexes of dethiobiotin synthetase, enzyme-diaminopelargonic acid-MgADP-AlF3 and enzyme-dethiobiotin-MgADP-Pi, respectively, have been determined to 1.8 A resolution. In dethiobiotin synthetase, AlF3 together with carb ...

    The crystal structures of two complexes of dethiobiotin synthetase, enzyme-diaminopelargonic acid-MgADP-AlF3 and enzyme-dethiobiotin-MgADP-Pi, respectively, have been determined to 1.8 A resolution. In dethiobiotin synthetase, AlF3 together with carbamylated diaminopelargonic acid mimics the phosphorylated reaction intermediate rather than the transition state complex for phosphoryl transfer. Observed differences in the binding of substrate, diaminopelargonic acid, and the product, dethiobiotin, suggest considerable displacements of substrate atoms during the ring closure step of the catalytic reaction. In both complexes, two metal ions are observed at the active site, providing evidence for a two-metal mechanism for this enzyme.


    Related Citations: 
    • Crystal Structure of an ATP-Dependent Carboxylase, Dethiobiotin Synthetase, at 1.65 A Resolution
      Huang, W.,Lindqvist, Y.,Schneider, G.,Gibson, K.J.,Flint, D.,Lorimer, G.
      (1994) Structure 2: 407
    • Snapshot of a Phosphorylated Substrate Intermediate by Kinetic Crystallography
      Kaeck, H.,Gibson, K.J.,Schneider, G.,Lindqvist, Y.
      (1998) Proc.Natl.Acad.Sci.USA 95: 5495


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (DETHIOBIOTIN SYNTHETASE)
A
224Escherichia coli (strain K12)Gene Names: bioD1
EC: 6.3.3.3
Find proteins for P13000 (Escherichia coli (strain K12))
Go to UniProtKB:  P13000
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DAA
Query on DAA

Download SDF File 
Download CCD File 
A
8-AMINO-7-CARBOXYAMINO-NONANOIC ACID WITH ALUMINUM FLUORIDE
C10 H19 Al F3 N2 O4
YXYIADHJEQLYPU-JWQBCWJNSA-J
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.900α = 90.00
b = 48.200β = 107.00
c = 60.900γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description