PDBsum entry 1bs1

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protein ligands metals links
Ligase PDB id
Protein chain
224 a.a. *
_MG ×2
Waters ×244
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Dethiobiotin synthetase complexed with dethiobiotin, adp , i phosphate and magnesium
Structure: Protein (dethiobiotin synthetase). Chain: a. Synonym: dtbs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.80Å     R-factor:   0.172     R-free:   0.206
Authors: H.Kaeck,J.Sandmark,K.J.Gibson,G.Schneider,Y.Lindqvist
Key ref:
H.Käck et al. (1998). Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis. Protein Sci, 7, 2560-2566. PubMed id: 9865950 DOI: 10.1002/pro.5560071209
31-Aug-98     Release date:   13-Jan-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P13000  (BIOD1_ECOLI) -  ATP-dependent dethiobiotin synthetase BioD 1
225 a.a.
224 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Dethiobiotin synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
+ 7,8-diaminononanoate
+ CO(2)
Bound ligand (Het Group name = ADP)
corresponds exactly
+ phosphate
Bound ligand (Het Group name = DAA)
matches with 75.00% similarity
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     biotin biosynthetic process   1 term 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1002/pro.5560071209 Protein Sci 7:2560-2566 (1998)
PubMed id: 9865950  
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-AlF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis.
H.Käck, J.Sandmark, K.J.Gibson, G.Schneider, Y.Lindqvist.
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.
  Selected figure(s)  
Figure 1.
Fig. 1. Reaction scheme for DTBS
Figure 2.
ig. 2. Initial differenceelectrondensity(contoured at 3r) attheactivesitein (A) the and (B) the DTBS-MgADP-DTB-Picomplex.
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1998, 7, 2560-2566) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16216072 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (2005).
Mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a CTP-inhibited complex.
  Biochemistry, 44, 13491-13499.
PDB code: 2ad5
15157079 J.A.Endrizzi, H.Kim, P.M.Anderson, and E.P.Baldwin (2004).
Crystal structure of Escherichia coli cytidine triphosphate synthetase, a nucleotide-regulated glutamine amidotransferase/ATP-dependent amidoligase fusion protein and homologue of anticancer and antiparasitic drug targets.
  Biochemistry, 43, 6447-6463.
PDB code: 1s1m
11896404 Madhusudan, P.Akamine, N.H.Xuong, and S.S.Taylor (2002).
Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase.
  Nat Struct Biol, 9, 273-277.
PDB code: 1l3r
10713991 K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
  Proteins, 38, 310-326.  
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