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Ligase PDB id
1dai
Jmol
Contents
Protein chain
219 a.a. *
Ligands
DSD
Waters ×135
* Residue conservation analysis
PDB id:
1dai
Name: Ligase
Title: Dethiobiotin synthetase complexed with 7-(carboxyamino)-8-am nonanoic acid
Structure: Dethiobiotin synthetase. Chain: a. Synonym: dtbs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.64Å     R-factor:   0.174    
Authors: W.Huang,J.Jia,G.Schneider,Y.Lindqvist
Key ref:
W.Huang et al. (1995). Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate. Biochemistry, 34, 10985-10995. PubMed id: 7669756 DOI: 10.1021/bi00035a004
Date:
08-May-95     Release date:   20-Jun-96    
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.
219 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
Bound ligand (Het Group name = DSD)
matches with 93.75% 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  

 

 
    reference    
 
 
DOI no: 10.1021/bi00035a004 Biochemistry 34:10985-10995 (1995)
PubMed id: 7669756  
 
 
Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on crystallographic studies of complexes with substrates and a reaction intermediate.
W.Huang, J.Jia, K.J.Gibson, W.S.Taylor, A.R.Rendina, G.Schneider, Y.Lindqvist.
 
  ABSTRACT  
 
The crystal structures of six complexes of homodimeric Escherichia coli dethiobiotin synthetase with a variety of substrates, substrate analogs, and products have been determined to high resolution. These include (1) the binary complex of dethiobiotin synthetase and the N7-carbamate of 7,8-diaminononanoic acid, (2) the binary complex of enzyme and the alternate substrate, 3-(1-aminoethyl)-nonanedioic acid, (3) the binary complex of enzyme with the product ADP, (4) the quaternary complex of enzyme, ADP, the N7-carbamate of 7,8-diaminononanoic acid, and Ca2+, (5) the ternary complex of enzyme, the ATP analog adenylyl (beta, gamma-methylene)diphosphonate, and the N7-carbamate of 7,8-diaminononanoic acid, and (6) the quaternary complex of enzyme, the ATP analog adenylyl (beta, gamma-methylene)diphosphonate, 7,8-diaminononanoic acid, and Mn2+. One molecule of each substrate binds to one monomer of the enzyme. ADP and the ATP analogue bind to the classical mononucleotide binding fold with the phosphate groups close to the phosphate binding loop Gly8--Thr16 between beta-strand beta 1 and the N-terminus of alpha-helix alpha 1. The adenine ring is bound in a pocket between beta-strands beta 6 and beta 7. In the quaternary complex with Mn2+, the metal binding site is found in the vicinity of the beta- and gamma-phosphate groups. Two oxygen atoms from the phosphates and oxygen atoms from the side chains of Asp54, Thr16, and Glu115 are ligands to the Mn2+ ion in the quaternary complex. In the complex with ADP and the N7-carbamate of 7,8-diaminononanoic acid prepared in the presence of Ca2+ ions, a different metal binding site is found. The Ca2+ ion is coordinated to an oxygen atom of the alpha-phosphate group of the nucleotide, the side chain of Asp54, and solvent molecules. The 7,8-diaminononanoic acid substrate molecule interacts with residues from both subunits, making the dimer the minimal functional unit. The diamino group binds between the loops after beta 2 and beta 4, and the terminal carboxyl group at the hydrophobic tail of the substrate interacts with the amino terminus of helix alpha 5 and with the side chain of Tyr187 in helix alpha 6 of the second subunit at the monomer-monomer interface. Strong additional electron density close to the N7 nitrogen atom of the 7,8-diaminononanoic acid substrate in some complexes indicates that, even in the absence of added bicarbonate in the crystallization mixture, the carbamylated intermediate is formed in the crystal.(ABSTRACT TRUNCATED AT 400 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17339319 S.R.Brinsmade, and J.C.Escalante-Semerena (2007).
In vivo and in vitro analyses of single-amino acid variants of the Salmonella enterica phosphotransacetylase enzyme provide insights into the function of its N-terminal domain.
  J Biol Chem, 282, 12629-12640.  
15880481 S.W.Van Arsdell, J.B.Perkins, R.R.Yocum, L.Luan, C.L.Howitt, N.P.Chatterjee, and J.G.Pero (2005).
Removing a bottleneck in the Bacillus subtilis biotin pathway: bioA utilizes lysine rather than S-adenosylmethionine as the amino donor in the KAPA-to-DAPA reaction.
  Biotechnol Bioeng, 91, 75-83.  
12218056 J.Sandmark, S.Mann, A.Marquet, and G.Schneider (2002).
Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin.
  J Biol Chem, 277, 43352-43358.
PDB codes: 1mly 1mlz
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.  
10966576 M.Y.Galperin, and N.V.Grishin (2000).
The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
  Proteins, 41, 238-247.  
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
10089517 H.Käck, K.J.Gibson, A.A.Gatenby, G.Schneider, and Y.Lindqvist (1998).
Purification and preliminary X-ray crystallographic studies of recombinant 7,8-diaminopelargonic acid synthase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 54, 1397-1398.  
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
9125495 G.Yang, T.Sandalova, K.Lohman, Y.Lindqvist, and A.R.Rendina (1997).
Active site mutants of Escherichia coli dethiobiotin synthetase: effects of mutations on enzyme catalytic and structural properties.
  Biochemistry, 36, 4751-4760.  
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
9214291 K.J.Gibson (1997).
Isolation and chemistry of the mixed anhydride intermediate in the reaction catalyzed by dethiobiotin synthetase.
  Biochemistry, 36, 8474-8478.  
  8763940 S.Bower, J.B.Perkins, R.R.Yocum, C.L.Howitt, P.Rahaim, and J.Pero (1996).
Cloning, sequencing, and characterization of the Bacillus subtilis biotin biosynthetic operon.
  J Bacteriol, 178, 4122-4130.  
8994880 Y.Lindqvist, and G.Schneider (1996).
Protein-biotin interactions.
  Curr Opin Struct Biol, 6, 798-803.  
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.