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Mann G, Stanger FV, Peschke T, Schroer K, Trung NQN, Burrer N, Grassinger F, Piccioni L, Erdogan O, Heimburger J, Koehl H, Ertle H, Denay R, Dreier P, Schlama T. Biocatalytic assembly of chemically modified oligonucleotides. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Enzymes have the potential to catalyse complex chemical reactions with unprecedented selectivity, under mild conditions in aqueous media. Accordingly, there is serious interest from the pharmaceutical industry to utilize enzymes as biocatalysts to produce medicines in an environmentally
sustainable and economic manner. Prominent advances in the field of biotechnology have transformed this potential into a reality. Using modern protein engineering techniques, in a matter of months it is possible to evolve an enzyme, which fits the demands of a chemical process, or even to
catalyse entirely novel chemistry. Consequently, biocatalysis is routinely applied throughout the pharmaceutical industry for a variety of applications, ranging from the manufacture of large volumes of high value blockbuster drugs to expanding the chemical space available for drug discovery.
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Stanger FV, de Beer TAP, Dranow DM, Schirmer T, Phan I, Dehio C. The BID Domain of Type IV Secretion Substrates Forms a Conserved Four-Helix Bundle Topped with a Hook. Structure 2016; 25:203-211. [PMID: 27889208 DOI: 10.1016/j.str.2016.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/07/2016] [Accepted: 10/25/2016] [Indexed: 10/20/2022]
Abstract
The BID (Bep intracellular delivery) domain functions as secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Bartonella effector proteins (Beps) during protein transfer into host cells infected by pathogenic Bartonella species. Furthermore, BID domains of Beps have often evolved secondary effector functions within host cells. Here, we provide crystal structures for three representative BID domains and describe a novel conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook. The conserved hydrophobic core provides a rigid scaffold to a surface that, despite a few conserved exposed residues and similarities in charge distribution, displays significant variability. We propose that the genuine function of BID domains as T4S signal may primarily depend on their rigid structure, while the plasticity of their surface may facilitate adaptation to secondary effector functions.
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Affiliation(s)
- Frédéric V Stanger
- Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland; Focal Area Structural Biology and Biophysics, Biozentrum University of Basel, 4056 Basel, Switzerland
| | - Tjaart A P de Beer
- Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease, The Center for Infectious Disease Research, Seattle, WA 98109, USA; Beryllium Discovery Corp., Bainbridge Island, WA 98110, USA
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum University of Basel, 4056 Basel, Switzerland.
| | - Isabelle Phan
- Seattle Structural Genomics Center for Infectious Disease, The Center for Infectious Disease Research, Seattle, WA 98109, USA
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum University of Basel, 4056 Basel, Switzerland.
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Abstract
The ubiquitous proteins with FIC (filamentation induced by cyclic AMP) domains use a conserved enzymatic machinery to modulate the activity of various target proteins by posttranslational modification, typically AMPylation. Following intensive study of the general properties of FIC domain catalysis, diverse molecular activities and biological functions of these remarkably versatile proteins are now being revealed. Here, we review the biological diversity of FIC domain proteins and summarize the underlying structure-function relationships. The original and most abundant genuine bacterial FIC domain proteins are toxins that use diverse molecular activities to interfere with bacterial physiology in various, yet ill-defined, biological contexts. Host-targeted virulence factors have evolved repeatedly out of this pool by exaptation of the enzymatic FIC domain machinery for the manipulation of host cell signaling in favor of bacterial pathogens. The single human FIC domain protein HypE (FICD) has a specific function in the regulation of protein stress responses.
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Affiliation(s)
- Alexander Harms
- Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; , ,
| | - Frédéric V Stanger
- Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; , , .,Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.,*Current address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; , ,
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Stanger FV, Dehio C, Schirmer T. Structure of the N-terminal Gyrase B fragment in complex with ADP⋅Pi reveals rigid-body motion induced by ATP hydrolysis. PLoS One 2014; 9:e107289. [PMID: 25202966 PMCID: PMC4159350 DOI: 10.1371/journal.pone.0107289] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022] Open
Abstract
Type II DNA topoisomerases are essential enzymes that catalyze topological rearrangement of double-stranded DNA using the free energy generated by ATP hydrolysis. Bacterial DNA gyrase is a prototype of this family and is composed of two subunits (GyrA, GyrB) that form a GyrA2GyrB2 heterotetramer. The N-terminal 43-kDa fragment of GyrB (GyrB43) from E. coli comprising the ATPase and the transducer domains has been studied extensively. The dimeric fragment is competent for ATP hydrolysis and its structure in complex with the substrate analog AMPPNP is known. Here, we have determined the remaining conformational states of the enzyme along the ATP hydrolysis reaction path by solving crystal structures of GyrB43 in complex with ADP⋅BeF3, ADP⋅Pi, and ADP. Upon hydrolysis, the enzyme undergoes an obligatory 12° domain rearrangement to accommodate the 1.5 Å increase in distance between the γ- and β-phosphate of the nucleotide within the sealed binding site at the domain interface. Conserved residues from the QTK loop of the transducer domain (also part of the domain interface) couple the small structural change within the binding site with the rigid body motion. The domain reorientation is reflected in a significant 7 Å increase in the separation of the two transducer domains of the dimer that would embrace one of the DNA segments in full-length gyrase. The observed conformational change is likely to be relevant for the allosteric coordination of ATP hydrolysis with DNA binding, cleavage/re-ligation and/or strand passage.
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Affiliation(s)
- Frédéric V. Stanger
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail:
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Goepfert A, Stanger FV, Dehio C, Schirmer T. Conserved inhibitory mechanism and competent ATP binding mode for adenylyltransferases with Fic fold. PLoS One 2013; 8:e64901. [PMID: 23738009 PMCID: PMC3667792 DOI: 10.1371/journal.pone.0064901] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 04/19/2013] [Indexed: 11/19/2022] Open
Abstract
The ubiquitous FIC domain is evolutionarily conserved from bacteria to human and has been shown to catalyze AMP transfer onto protein side-chain hydroxyl groups. Recently, it was predicted that most catalytically competent Fic proteins are inhibited by the presence of an inhibitory helix αinh that is provided by a cognate anti-toxin (class I), or is part of the N- or C-terminal part of the Fic protein itself (classes II and III). In vitro, inhibition is relieved by mutation of a conserved glutamate of αinh to glycine. For the class III bacterial Fic protein NmFic from Neisseria meningitidis, the inhibitory mechanism has been elucidated. Here, we extend above study by including bacterial class I and II Fic proteins VbhT from Bartonella schoenbuchensis and SoFic from Shewanella oneidensis, respectively, and the respective E->G mutants. Comparative enzymatic and crystallographic analyses show that, in all three classes, the ATP substrate binds to the wild-type FIC domains, but with the α-phosphate in disparate and non-competent orientations. In the E->G mutants, however, the tri-phosphate moiety is found reorganized to the same tightly bound structure through a unique set of hydrogen bonds with Fic signature motif residues. The γ-phosphate adopts the location that is taken by the inhibitory glutamate in wild-type resulting in an α-phosphate orientation that can be attacked in-line by a target side-chain hydroxyl group. The latter is properly registered to the Fic active center by main-chain β-interactions with the β-hairpin flap. These data indicate that the active site motif and the exposed edge of the flap are both required to form an adenylylation-competent Fic protein.
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Affiliation(s)
- Arnaud Goepfert
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Frédéric V. Stanger
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail: (TS); (CD)
| | - Tilman Schirmer
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail: (TS); (CD)
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