Crystal structure of a putative modulator of DNA gyrase (pmbA) from <i>Thermotoga maritima</i> at 1.95 Å resolution reveals a new fold

Rife, Chris; Schwarzenbacher, Robert; McMullan, Daniel; Abdubek, Polat; Ambing, Eileen; Axelrod, Herbert L.; Biorac, Tanya; Cánaves, Jaume M.; Chiu, Hsiu‐Ju; Deacon, Ashley M.; DiDonato, Michael; Elsliger, Marc‐André; Godzik, Adam; Grittini, Carina; Grzechnik, Slawomir K.; Hale, Joanna; Hampton, Eric; Han, Gye Won; Haugen, Justin; Hornsby, Michael; Jaroszewski, Lukasz; Klock, Heath E.; Koesema, Eric; Kreusch, Andreas; Kühn, Peter; Lesley, Scott A.; Miller, Mitchell D.; Moy, Kin; Nigoghossian, Edward; Paulsen, Jessica; Quijano, Kevin; Reyes, Ron; Sims, Eric; Spraggon, Glen; Stevens, Raymond C.; Bedem, Henry van den; Velasquez, Jeff; Vincent, Juli; White, Aprilfawn; Wolf, Guenter; Xu, Qingping; Wooley, John; Wilson, Ian A.

doi:10.1002/prot.20468

Cited by 10 publications

(7 citation statements)

References 16 publications

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“…The sequence of E. coli TldE differs by only two amino acids from that of Shigella flexneri PmbA, and thus the E. coli TldE monomer superposes well upon a monomer from the S. flexneri PmbA homodimer (PDB: 3TV9 ; root-mean-square deviation [RMSD] = 0.84 Å). As described for Thermotoga maritima PmbA (PDB: 1VL4 ; Rife et al., 2005 ), the subunit is divided into two domains, each accounting for roughly half of the primary sequence. The N-terminal domain is pseudo 2-fold symmetric, being comprised of a very long and curved six-stranded anti-parallel β sheet with a pair of α helices at each end lying against the convex outer surface of the sheet.…”

Section: Resultsmentioning

confidence: 99%

“…To date, structural information has only been available for the TldE protein, with four representative structures from Thermotoga maritima (PDB: 1VL4 ; Rife et al., 2005 ), Pseudomonas aeruginosa (PDB: 3QTD ), Shigella flexneri (PDB: 3TV9 ), and Bacteroides thetaiotaomicron (PDB: 1VPB ). All these proteins form roughly spherical homodimers with a hollow core and none possesses any recognizable catalytic site or shows biological activity.…”

Section: Introductionmentioning

confidence: 99%

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The Origins of Specificity in the Microcin-Processing Protease TldD/E

et al. 2017

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SummaryTldD and TldE proteins are involved in the biosynthesis of microcin B17 (MccB17), an Escherichia coli thiazole/oxazole-modified peptide toxin targeting DNA gyrase. Using a combination of biochemical and crystallographic methods we show that E. coli TldD and TldE interact to form a heterodimeric metalloprotease. TldD/E cleaves the N-terminal leader sequence from the modified MccB17 precursor peptide, to yield mature antibiotic, while it has no effect on the unmodified peptide. Both proteins are essential for the activity; however, only the TldD subunit forms a novel metal-containing active site within the hollow core of the heterodimer. Peptide substrates are bound in a sequence-independent manner through β sheet interactions with TldD and are likely cleaved via a thermolysin-type mechanism. We suggest that TldD/E acts as a “molecular pencil sharpener”: unfolded polypeptides are fed through a narrow channel into the active site and processively truncated through the cleavage of short peptides from the N-terminal end.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The Origins of Specificity in the Microcin-Processing Protease TldD/E

et al. 2017

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“…The cell death is ‘addicted’ to the short-lived CcdA such that cells rely on the de novo synthesis of CcdA to survive. While investigation of tldD/E deletion mutants suggested that both proteins could be involved in degradation of the CcdA antitoxin in vivo [17], crystallographic analysis of Thermotoga maritima TldE (PmbA) failed to detect any co-ordinates for metal ions in the protein structure or any structural domain of a hydrolase [18]. Since there has not been any report on biochemical characterization of a TldD/E homologue in the current literature, whether or not any TldD or TldE encodes a protease remains to be tested.…”

Section: Introductionmentioning

confidence: 99%

An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease

Peng

Han

et al. 2012

Bioscience Reports

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A putative protease gene (tldD) was previously identified from studying tolerance of letD encoding the CcdB toxin of a toxin–antidote system of the F plasmid in Escherichia coli. While this gene is evolutionarily conserved in archaea and bacteria, the proteolytic activity of encoded proteins remained to be demonstrated experimentally. Here we studied Sso0660, an archaeal TldD homologue encoded in Sulfolobus solfataricus by overexpression of the recombinant protein and characterization of the purified enzyme. We found that the enzyme is active in degrading azocasein and FITC–BSA substrates. Protease inhibitor studies showed that EDTA and o-phenanthroline, two well-known metalloprotease inhibitors, either abolished completely or strongly inhibited the enzyme activity, and flame spectrometric analysis showed that a zinc ion is a cofactor of the protease. Furthermore, the protein forms disulfide bond via the Cys416 residue, yielding protein dimer that is the active form of the enzyme. These results establish for the first time that tidD genes encode zinc-containing proteases, classifying them as a family in the metalloprotease class.

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“…Like other protease family members, one subunit of TkTldE contained 11 α-helices and 21 β-strands ( Figure 2B). As described for PmbA (PDB: 1VL4) [18] and E. coli TldD and TldE (PDB: 5NJ9) [15], one subunit of TkTldE contained two domains. The N-terminal domain was composed of six anti-parallel β-strands and five α-helices distributing on the outer surface of β-sheet.…”

Section: Resultsmentioning

confidence: 99%

“…TldD/TldE from archaebacteria were different to those from eubacteria. The structure of a putative modulator of DNA gyrase (TldE) from Thermotoga maritima was reported, but shed little light on its functions as a modulator of DNA gyrase [18]. Sso0660 from Sulfolobus solfataricus, a TldD homologue, could function alone as a metalloprotease, as it could proteolytically degrade azocasein and FITC-BSA substrates with a zinc ion as its cofactor [14].…”

Section: Introductionmentioning

confidence: 99%

Crystal Structure of a Putative Modulator of Gyrase (TldE) from Thermococcus kodakarensis

Zhang

Zhao

et al. 2019

Crystals

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TldD and TldE proteins interact and form a complex to degrade unfolded peptides. The gene Tk0499 from Thermococcus kodakarensis encoded a putative modulator of gyrase (TkTldE). Although TldE genes were common in bacteria and archaea, the structural basis on the evolution of proteins remained largely unknown. Here, the three-dimensional structure of TkTldE was determined by X-ray diffraction. Crystals were acquired by the sitting-drop vapor-diffusion method. X-ray diffraction data from crystals were collected at 2.35 Å. The space group and unit-cell parameters suggested that there were two molecules in the asymmetric unit. Our results showed that TkTldE forms a homodimer, which contained anti-parallel β-strands and a pair of α-helices. Comparison of the structures of TldE and TldD showed that despite their high sequence similarity, TldE lacked the conserved HExxxH and GxC motif in which two His and a Cys residues bound a metal ion. Taken together, these results provided insight into the structural information of this class of TldE/TldD.

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Crystal structure of a putative modulator of DNA gyrase (pmbA) from Thermotoga maritima at 1.95 Å resolution reveals a new fold

Cited by 10 publications

References 16 publications

The Origins of Specificity in the Microcin-Processing Protease TldD/E

The Origins of Specificity in the Microcin-Processing Protease TldD/E

An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease

Crystal Structure of a Putative Modulator of Gyrase (TldE) from Thermococcus kodakarensis

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