1DAM | pdb_00001dam

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

• PDB DOI: https://doi.org/10.2210/pdb1DAM/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-08-31 Released: 1999-01-13 
• Deposition Author(s): Kaeck, H., Sandmark, J., Gibson, K.J., Schneider, G., Lindqvist, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.200 (DCC) 

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

• PubMed: 9865950 
• DOI: https://doi.org/10.1002/pro.5560071209
• Primary Citation of Related Structures:  
  1BS1, 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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 24.81 kDa 
• Atom Count: 1,940 
• Modelled Residue Count: 224 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DETHIOBIOTIN SYNTHETASE)	A	224	Escherichia coli	Mutation(s): 0  EC: 6.3.3.3
UniProt
Find proteins for P13000 (Escherichia coli (strain K12)) Explore P13000  Go to UniProtKB:  P13000

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
DTB	F [auth A]	6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID C10 H18 N2 O3 AUTOLBMXDDTRRT-JGVFFNPUSA-N
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.200 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.7	α = 90
b = 48.9	β = 106.7
c = 61.1	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Kaeck, H., Sandmark, J., Gibson, K.J., Schneider, G., Lindqvist, Y.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2016-04-06
  Changes: Non-polymer description
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references, Derived calculations