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PDBsum entry 1dbs

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Biotin biosynthesis PDB id
1dbs
Jmol
Contents
Protein chain
224 a.a. *
Ligands
SO4 ×3
Waters ×201
* Residue conservation analysis
PDB id:
1dbs
Name: Biotin biosynthesis
Title: Mechanistic implications and family relationships from the structure of dethiobiotin synthetase
Structure: Dethiobiotin synthetase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.179    
Authors: L.Sawyer,D.Alexeev
Key ref:
D.Alexeev et al. (1994). Mechanistic implications and family relationships from the structure of dethiobiotin synthetase. Structure, 2, 1061-1072. PubMed id: 7881906 DOI: 10.1016/S0969-2126(94)00109-X
Date:
29-Nov-94     Release date:   20-Apr-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.6.3.3.3  - Dethiobiotin synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + 7,8-diaminononanoate + CO2 = ADP + phosphate + dethiobiotin
ATP
+ 7,8-diaminononanoate
+ CO(2)
= ADP
+ phosphate
+ dethiobiotin
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  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(94)00109-X Structure 2:1061-1072 (1994)
PubMed id: 7881906  
 
 
Mechanistic implications and family relationships from the structure of dethiobiotin synthetase.
D.Alexeev, R.L.Baxter, L.Sawyer.
 
  ABSTRACT  
 
BACKGROUND: Biotin is the vitamin essential for many biological carboxylation reactions, such as the conversion of acetyl-coenzyme A (CoA) to malonyl-CoA in fatty acid biosynthesis. Dethiobiotin synthetase (DTBS) facilitates the penultimate, ureido ring closure in biotin synthesis, which is a non-biotin-dependent carboxylation. DTBS displays no sequence similarity to any other protein in the database. Structural studies provide a molecular insight into the reaction mechanism of DTBS. RESULTS: We present the structure of DTBS refined to 1.80 A resolution with an R-factor of 17.2% for all terms plus unrefined data on the binding of the substrate, 7,8-diaminopelargonic acid and the product, dethiobiotin. These studies confirm that the protein forms a homodimer with each subunit folded as a single globular alpha/beta domain. The presence of sulphate ions in the crystals and comparisons with the related Ha-ras-p21 oncogene product are used to infer the ATP-binding site, corroborated by the difference electron density for the ATP analogue AMP-PNP. CONCLUSIONS: This study establishes that the enzyme active site is situated at the dimer interface, with the substrate binding to one monomer and ATP to the other. The overall fold of DTBS closely resembles that of three other enzymes, adenylosuccinate synthetase (purA), Ha-ras-p21, and nitrogenase iron protein, that are unrelated by sequence or function, indicating that DTBS is a member of a diverse family of enzymes.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The scheme of the reaction mechanism of dethiobiotin synthetase (see text for details). Figure 1. The scheme of the reaction mechanism of dethiobiotin synthetase (see text for details).
Figure 3.
Figure 3. The topology of DTBS compared with that of Ha-ras-p21, adenylo succinate synthetase (purA), and the nitrogenase iron protein fromAzotobacter vinelandii (NIP). The quaternary structures are shown schematically on the right. GAP is the GTPase activating protein. The shaded elements represent the regions of spatial overlap of the proteins. Figure 3. The topology of DTBS compared with that of Ha-ras-p21, adenylo succinate synthetase (purA), and the nitrogenase iron protein fromAzotobacter vinelandii (NIP). The quaternary structures are shown schematically on the right. GAP is the GTPase activating protein. The shaded elements represent the regions of spatial overlap of the proteins.
 
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 1061-1072) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
  10211841 A.Marina, P.M.Alzari, J.Bravo, M.Uriarte, B.Barcelona, I.Fita, and V.Rubio (1999).
Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.
  Protein Sci, 8, 934-940.
PDB codes: 1b7b 2we4 2we5
10089457 T.Sandalova, G.Schneider, H.Käck, and Y.Lindqvist (1999).
Structure of dethiobiotin synthetase at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 55, 610-624.
PDB code: 1byi
  9865950 H.Käck, J.Sandmark, K.J.Gibson, G.Schneider, and Y.Lindqvist (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.
PDB codes: 1bs1 1dam
9576910 H.Käck, K.J.Gibson, Y.Lindqvist, and G.Schneider (1998).
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
  Proc Natl Acad Sci U S A, 95, 5495-5500.
PDB codes: 1a82 1dak
9218784 J.A.Bertrand, G.Auger, E.Fanchon, L.Martin, D.Blanot, J.van Heijenoort, and O.Dideberg (1997).
Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.
  EMBO J, 16, 3416-3425.
PDB codes: 1e0d 1uag
8663109 B.W.Poland, Z.Hou, C.Bruns, H.J.Fromm, and R.B.Honzatko (1996).
Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli.
  J Biol Chem, 271, 15407-15413.
PDB codes: 1hon 1hoo 1hop
8994880 Y.Lindqvist, and G.Schneider (1996).
Protein-biotin interactions.
  Curr Opin Struct Biol, 6, 798-803.  
8591031 D.Alexeev, R.L.Baxter, O.Smekal, and L.Sawyer (1995).
Substrate binding and carboxylation by dethiobiotin synthetase--a kinetic and X-ray study.
  Structure, 3, 1207-1215.  
7592948 R.H.Mosher, D.J.Camp, K.Yang, M.P.Brown, W.V.Shaw, and L.C.Vining (1995).
Inactivation of chloramphenicol by O-phosphorylation. A novel resistance mechanism in Streptomyces venezuelae ISP5230, a chloramphenicol producer.
  J Biol Chem, 270, 27000-27006.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.