Mechanistic implications and family relationships from the structure of dethiobiotin synthetase

Alexeev, Dmitry; Baxter, Robert L.; Sawyer, Lindsay

doi:10.1016/s0969-2126(94)00109-x

Cited by 30 publications

(29 citation statements)

References 45 publications

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“…Comparison of the DTBS structure at room temperature and at low temperature A number of crystal structures of DTBS have been determined ± these include the free enzyme (Huang et al, 1994;Alexeev et al, 1994) and various complexes with substrates, analogues and reaction intermediates (Huang et al, 1995;Alexeev et al, 1995;Ka È ck et al, 1998). Of particular interest is the structure of the unliganded enzyme determined at room temperature at 1.65 A Ê resolution, using crystals obtained under the same conditions as in this study.…”

Section: Acta Cryst (1999) D55 610±624mentioning

confidence: 99%

“…DTBS is a homodimer composed of 224 amino-acid residues per subunit. Crystallographic studies of dethiobiotin synthetase have revealed that the structure of the enzyme subunit consists of one domain folded into a sevenstranded parallel -sheet¯anked by helices (Huang et al, 1994;Alexeev et al, 1994). Subsequent crystallographic studies of binary, ternary and quaternary complexes of DTBS with various substrates and substrate analogues (Huang et al, 1995;Alexeev et al, 1995) have led to considerable mechanistic insights.…”

Section: Introductionmentioning

confidence: 99%

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Structure of dethiobiotin synthetase at 0.97 Å resolution

Sandalova¹,

Schneider²,

Käck³

et al. 1999

Acta Crystallogr D Biol Crystallogr

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The crystal structure of the 224-residue protein dethiobiotin synthetase from Escherichia coli has been re®ned using X-ray diffraction data at 0.97 A Ê resolution at 100 K. The model, consisting of 4143 protein atoms including 1859 H atoms and 436 solvent sites, was re®ned to a ®nal R factor of 11.6% for all re¯ections, and has an estimated mean standard uncertainty for the atomic positions of 0.022 A Ê , derived from inversion of the blocked matrix. The structure was re®ned with a full anisotropic model for the atomic displacement parameters using SHELX97. Stereochemical restraints were applied throughout the re®nement. In the last cycles, the planarity of the peptide bonds was not restrained, resulting in a mean 3 value of 179.6. Analysis of the most anisotropic regions of the protein shows that they form four clusters of residues. Alternate conformations for the side chains of 15 residues and for the main-chain atoms of six residues from three loops were included in the model. An analysis of CÐHÁ Á ÁO hydrogen bonds shows that such interactions occur rather frequently in DTBS; in total, 16 such hydrogen bonds were found. In the central -sheet, 13 CÐHÁ Á ÁO bonds between carbonyl O and C H atoms were found. Other interactions of this type involve main-chain±side-chain and side-chain±side-chain CÐHÁ Á ÁO bonds. The model includes 436 water sites, of which 233 molecules form the ®rst hydration shell. Analysis of the protein±solvent interactions shows that about one third of the accessible surface of the enzyme is not covered by ordered solvent. No difference in propensity for ordered solvent close to hydrophilic or hydrophobic surface areas was found. The comparison of the 100 K structure with the structure of the enzyme determined at room temperature shows several regions with different conformation, including areas in the active site, suggesting that structural transitions can occur during¯ash freezing. This observation questions one of the basic assumptions in the analysis of enzymatic reaction mechanisms using cryocrystallography.

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Section: Acta Cryst (1999) D55 610±624mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Structure of dethiobiotin synthetase at 0.97 Å resolution

Sandalova¹,

Schneider²,

Käck³

et al. 1999

Acta Crystallogr D Biol Crystallogr

View full text Add to dashboard Cite

show abstract

“…1a) 7 . The x-ray structures and catalytic mechanisms of the E. coli AONS, DANS, DTBS and BS enzymes have been reported [8][9][10][11][12][13] .…”

Section: Introductionmentioning

confidence: 99%

Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters

et al. 2017

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Biotin is an essential vitamin in plants and mammals functioning as the carbon dioxide carrier within central lipid metabolism. Bacterial pimeloyl-CoA synthetase (BioW) acts as a highly specific substrate selection gate ensuring the integrity of the carbon chain in biotin synthesis.BioW catalyses the condensation of pimelic acid (C7 dicarboxylic acid) with CoASH in an ATP dependent manner to form pimeloyl-CoA, the first dedicated biotin building block.Multiple structures of Bacillus subtilis BioW together capture all three substrates as well as the intermediate pimeloyl-adenylate and product pyrophosphate (PP i ), and indicates that the enzyme uses an internal ruler to select the correct dicarboxylic acid substrate. Both the catalytic mechanism and the surprising stability of the adenylate intermediate were rationalized through site-directed mutagenesis. Building on this understanding, BioW was engineered to synthesise high value heptanoyl (C7) and octanoyl (C8) mono carboxylic acidCoA and C8 dicarboxylic-CoA products, highlighting the enzyme's synthetic potential.2

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“…The P-loop motif occurs in a wide variety of proteins that, although diverse in biochemical function, have both a common nucleotide binding sequence and similar structures (Saraste et al, 1990;Schulz, 1992). Among these are the human Ha-ras p21 protein, E. coli adenylate kinase, EF-Tu and dethiobiotin synthetase (Jurnak, 1985;Pai et al, 1989Pai et al, , 1990Muller and Schulz, 1992;Huang et al, 1994;Alexeev et al, 1994). The ATP-binding site is also present in the transport protein superfamily that includes the cystic fibrosis gene product (Hyde et al, 1990;Mimura et al, 1991).…”

mentioning

confidence: 99%