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PDBsum entry 1a82

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protein ligands metals links
Biotin biosynthesis PDB id
1a82
Jmol
Contents
Protein chain
224 a.a. *
Ligands
DNN
ATP
Metals
_MG
Waters ×219
* Residue conservation analysis
PDB id:
1a82
Name: Biotin biosynthesis
Title: Dethiobiotin synthetase from escherichia coli, complex with atp and diaminopelargonic acid
Structure: Dethiobiotin synthetase. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.190     R-free:   0.246
Authors: H.Kaeck,K.J.Gibson,Y.Lindqvist,G.Schneider
Key ref:
H.Käck et al. (1998). Snapshot of a phosphorylated substrate intermediate by kinetic crystallography. Proc Natl Acad Sci U S A, 95, 5495-5500. PubMed id: 9576910 DOI: 10.1073/pnas.95.10.5495
Date:
31-Mar-98     Release date:   11-May-99    
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
Bound ligand (Het Group name = ATP)
corresponds exactly
+
7,8-diaminononanoate
Bound ligand (Het Group name = DNN)
corresponds exactly
+ 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: 10.1073/pnas.95.10.5495 Proc Natl Acad Sci U S A 95:5495-5500 (1998)
PubMed id: 9576910  
 
 
Snapshot of a phosphorylated substrate intermediate by kinetic crystallography.
H.Käck, K.J.Gibson, Y.Lindqvist, G.Schneider.
 
  ABSTRACT  
 
The ATP-dependent enzyme dethiobiotin synthetase from Escherichia coli catalyses the formation of dethiobiotin from CO2 and 7, 8-diaminopelargonic acid. The reaction is initiated by the formation of a carbamate and proceeds through a phosphorylated intermediate, a mixed carbamic phosphoric anhydride. Here, we report the crystal structures at 1.9- and 1.6-A resolution, respectively, of the enzyme-MgATP-diaminopelargonic acid and enzyme-MgADP-carbamic-phosphoric acid anhydride complexes, observed by using kinetic crystallography. Reaction initiation by addition of either NaHCO3 or diaminopelargonic acid to crystals already containing cosubstrates resulted in the accumulation of the phosphorylated intermediate at the active site. The phosphoryl transfer step shows inversion of the configuration at the phosphorus atom, consistent with an in-line attack by the carbamate oxygen onto the phosphorus atom of ATP. A key feature in the structure of the complex of the enzyme with the reaction intermediate is two magnesium ions, bridging the phosphates at the cleavage site. These magnesium ions compensate the negative charges at both phosphate groups after phosphoryl transfer and contribute to the stabilization of the reaction intermediate.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Polar interactions of the substrate (a) and the reaction intermediate (b) with protein atoms at the active site of DTBS. Hydrogen bonds (cutoff distance 3.2 Å) are shown with dotted lines. Coordination bonds from atoms of the protein and the substrate/reaction intermediate to the Mg2+ ions are included.
Figure 6.
Fig. 6. Refined structure of the metal sites of the complex of DTBS with ADP and a reaction intermediate, the mixed carbamic-phosphoric acid anhydride. Golden spheres indicate magnesium ions, and red spheres indicate solvent molecules. Coordination bonds are shown by dotted lines.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20606259 G.Bujacz, B.Wrzesniewska, and A.Bujacz (2010).
Cryoprotection properties of salts of organic acids: a case study for a tetragonal crystal of HEW lysozyme.
  Acta Crystallogr D Biol Crystallogr, 66, 789-796.  
20700534 P.F.Gherardini, G.Ausiello, and M.Helmer-Citterich (2010).
Superpose3D: a local structural comparison program that allows for user-defined structure representations.
  PLoS One, 5, 0.  
20164644 S.Westenhoff, E.Nazarenko, E.Malmerberg, J.Davidsson, G.Katona, and R.Neutze (2010).
Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches.
  Acta Crystallogr A, 66, 207-219.  
19948960 G.Bozkurt, G.Stjepanovic, F.Vilardi, S.Amlacher, K.Wild, G.Bange, V.Favaloro, K.Rippe, E.Hurt, B.Dobberstein, and I.Sinning (2009).
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
  Proc Natl Acad Sci U S A, 106, 21131-21136.
PDB codes: 3iqw 3iqx
18562298 A.V.Cherepanov, E.V.Doroshenko, J.Matysik, S.de Vries, and H.J.de Groot (2008).
The associative nature of adenylyl transfer catalyzed by T4 DNA ligase.
  Proc Natl Acad Sci U S A, 105, 8563-8568.  
18065529 E.S.Rangarajan, A.Asinas, A.Proteau, C.Munger, J.Baardsnes, P.Iannuzzi, A.Matte, and M.Cygler (2008).
Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF.
  J Bacteriol, 190, 1447-1458.
PDB codes: 2i6r 2rb9
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
10572011 S.Wang, K.Karbstein, A.Peracchi, L.Beigelman, and D.Herschlag (1999).
Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate.
  Biochemistry, 38, 14363-14378.  
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
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 codes are shown on the right.