PDBsum entry 1dts

Cyclo-ligase

PDB id: 1dts

Contents

Protein chain

220 a.a. *

Waters ×189

* Residue conservation analysis

PDB id:

1dts

Name:

Cyclo-ligase

Title:

Crystal structure of an atp dependent carboxylase, dethiobiotin synthase, at 1.65 angstroms resolution

Structure:

Dethiobiotin synthetase. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.65Å R-factor: 0.169 R-free: 0.230

Authors:

W.Huang,Y.Lindqvist,G.Schneider

Key ref:

W.Huang et al. (1994). Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution. Structure, 2, 407-414. PubMed id: 8081756 DOI: 10.1016/S0969-2126(00)00042-3

Date:

28-Mar-95 Release date: 20-Apr-95

Protein chain

P13000  (BIOD1_ECOLI) -  ATP-dependent dethiobiotin synthetase BioD 1 from Escherichia coli (strain K12)

Seq: 225 a.a.

Struc: 220 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.3.3 - dethiobiotin synthase.
• Reaction: (7R,8S)-7,8-diammoniononanoate + CO2 + ATP = (4R,5S)-dethiobiotin + ADP + phosphate + 3 H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0969-2126(00)00042-3

Structure 2:407-414 (1994)

PubMed id: 8081756

Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution.

W.Huang, Y.Lindqvist, G.Schneider, K.J.Gibson, D.Flint, G.Lorimer.

ABSTRACT

BACKGROUND: In Escherichia coli, the enzymes of the biotin biosynthesis pathway are encoded by the bio operon. One of these enzymes, ATP-dependent dethiobiotin synthetase, catalyzes the carboxylation of 7,8-diaminopelargonic acid leading to the formation of the ureido ring of biotin. The enzyme belongs to the class of ATP-dependent carboxylases and we present here the first crystal structure determined for this class of enzyme. RESULTS: We have determined the crystal structure of homodimeric dethiobiotin synthetase to 1.65 A resolution. The subunit consists of a seven-stranded parallel beta-sheet, surrounded by alpha-helices. The sheet contains the classical mononucleotide-binding motif with a fingerprint peptide Gly-X-X-X-X-X-Gly-Lys-Thr. The mononucleotide binding part of the structure is very similar to the GTP-binding protein H-ras-p21 and thus all GTP-binding proteins. A comparison reveals that some of the residues, which in H-ras-p21 interact with the nucleotide and the metal ion, are conserved in the synthetase. CONCLUSIONS: The three-dimensional structure of dethiobiotin synthetase has revealed that ATP-dependent carboxylases contain the classical mononucleotide-binding fold. Considerable similarities to the structure of the GTP-binding protein H-ras-p21 were found, indicating that both proteins might have evolved from a common ancestral mononucleotide-binding fold.

Selected figure(s)

Figure 9.
Figure 9. Schematic view of the dimer of dethiobiotin synthetase. The color scheme is that used in Figure 4 and Figure 5. Conserved side chains at the subunit–subunit interface are included in ball- and-stick representation (for details see text). The picture was generated with the program MOLSCRIPT [21]. Figure 9. Schematic view of the dimer of dethiobiotin synthetase. The color scheme is that used in [3]Figure 4 and [4]Figure 5. Conserved side chains at the subunit–subunit interface are included in ball- and-stick representation (for details see text). The picture was generated with the program MOLSCRIPT [[5]21].

Figure 11.
Figure 11. Schematic view of the active site of dethiobiotin synthetase. The color scheme is that used for Figure 4 and Figure 5. Conserved polar residues in the vicinity of the suggested binding site of the γ -phosphate of ATP are shown. The picture was generated with the program MOLSCRIPT [21]. Figure 11. Schematic view of the active site of dethiobiotin synthetase. The color scheme is that used for [3]Figure 4 and [4]Figure 5. Conserved polar residues in the vicinity of the suggested binding site of the γ -phosphate of ATP are shown. The picture was generated with the program MOLSCRIPT [[5]21].

The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 407-414) copyright 1994.

Figures were selected by an automated process.