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| - | <!-- | + | ==Solution structure of the bacterial antidote ParD== |
| - | The line below this paragraph, containing "STRUCTURE_2an7", creates the "Structure Box" on the page.
| + | <StructureSection load='2an7' size='340' side='right'caption='[[2an7]]' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2an7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AN7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AN7 FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | --> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2an7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2an7 OCA], [https://pdbe.org/2an7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2an7 RCSB], [https://www.ebi.ac.uk/pdbsum/2an7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2an7 ProSAT]</span></td></tr> |
| - | {{STRUCTURE_2an7| PDB=2an7 | SCENE= }}
| + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PARD_ECOLX PARD_ECOLX] Antitoxin component of a toxin-antitoxin (TA) module involved in plasmid partition. Inhibits the anti-DNA gyrase activity of toxin ParE; reverses and restores gyrase catalytic activity in vitro. The parDE operon alone is capable of stabilizing an RK2-derived minireplicon under defined growth conditions in several different Gram-negative bacteria. It does so by the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds its own promoter, autorepressing it; gentically only ParD is required for full autorepression.<ref>PMID:12010492</ref> <ref>PMID:1459960</ref> <ref>PMID:8133518</ref> <ref>PMID:8631720</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | ParD is the antidote of the plasmid-encoded toxin-antitoxin (TA) system ParD-ParE. These modules rely on differential stabilities of a highly expressed but labile antidote and a stable toxin expressed from one operon. Consequently, loss of the coding plasmid results in loss of the protective antidote and poisoning of the cell. The antidote protein usually also exhibits an autoregulatory function of the operon. In this paper, we present the solution structure of ParD. The repressor activity of ParD is mediated by the N-terminal half of the protein, which adopts a ribbon-helix-helix (RHH) fold. The C-terminal half of the protein is unstructured in the absence of its cognate binding partner ParE. Based on homology with other RHH proteins, we present a model of the ParD-DNA interaction, with the antiparallel beta-strand being inserted into the major groove of DNA. The fusion of the N-terminal DNA-binding RHH motif to the toxin-binding unstructured C-terminal domain is discussed in its evolutionary context. |
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| - | '''Solution structure of the bacterial antidote ParD'''
| + | The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.,Oberer M, Zangger K, Gruber K, Keller W Protein Sci. 2007 Aug;16(8):1676-88. PMID:17656583<ref>PMID:17656583</ref> |
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| - | | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | ==Overview==
| + | </div> |
| - | NMR and CD spectroscopy have been used to characterize, both structurally and dynamically, the 82-amino-acid ParD protein of the post-segregational killing module of the broad-host-range plasmid RP4/RK2. ParD occurs as a dimer in solution and exercises two different control functions; an autoregulatory function by binding to its own promoter P(parDE) and a plasmid-stabilizing function by inhibiting ParE toxicity in cells that express ParD and ParE. Analysis of the secondary structure based on the chemical-shift indices, sequential nuclear Overhauser enhancements (NOEs) and (3)J(Halpha-NH) scalar coupling constants showed that the N-terminal domain of ParD consists of a short beta-ribbon followed by three alpha-helices, demonstrating that ParD contains a ribbon-helix-helix fold, a DNA-binding motif found in a family of small prokaryotic repressors. (15)N longitudinal (T(1)) and transverse (T(2)) relaxation measurements and hetero nuclear NOEs showed that ParD is divided into two separate domains, a well-ordered N-terminal domain and a very flexible C-terminal domain. An increase in secondary structure was observed upon addition of trifluoroethanol, suggested to result from the formation of structured stretches in the C-terminal part of the protein. This is the first experimental evidence that the DNA-binding domain of ParD belongs to the ribbon-helix-helix fold family, and this structural motif is proposed to be present in functionally similar antidote proteins.
| + | <div class="pdbe-citations 2an7" style="background-color:#fffaf0;"></div> |
| - | | + | == References == |
| - | ==About this Structure== | + | <references/> |
| - | 2AN7 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AN7 OCA].
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | ==Reference== | + | |
| - | The anti-toxin ParD of plasmid RK2 consists of two structurally distinct moieties and belongs to the ribbon-helix-helix family of DNA-binding proteins., Oberer M, Zangger K, Prytulla S, Keller W, Biochem J. 2002 Jan 1;361(Pt 1):41-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11743881 11743881]
| + | |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Gruber, K.]] | + | [[Category: Gruber K]] |
| - | [[Category: Keller, W.]] | + | [[Category: Keller W]] |
| - | [[Category: Oberer, M.]] | + | [[Category: Oberer M]] |
| - | [[Category: Zangger, K.]] | + | [[Category: Zangger K]] |
| - | [[Category: Bacterial antidote]]
| + | |
| - | [[Category: Dna-binding motif]]
| + | |
| - | [[Category: Plasmid addiction]]
| + | |
| - | [[Category: Ribbon-helix-helix]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 19:14:49 2008''
| + | |
| Structural highlights
Function
PARD_ECOLX Antitoxin component of a toxin-antitoxin (TA) module involved in plasmid partition. Inhibits the anti-DNA gyrase activity of toxin ParE; reverses and restores gyrase catalytic activity in vitro. The parDE operon alone is capable of stabilizing an RK2-derived minireplicon under defined growth conditions in several different Gram-negative bacteria. It does so by the post-segregational killing (PSK) of plasmid-free cells, also referred to as a plasmid addiction system. Binds its own promoter, autorepressing it; gentically only ParD is required for full autorepression.[1] [2] [3] [4]
Publication Abstract from PubMed
ParD is the antidote of the plasmid-encoded toxin-antitoxin (TA) system ParD-ParE. These modules rely on differential stabilities of a highly expressed but labile antidote and a stable toxin expressed from one operon. Consequently, loss of the coding plasmid results in loss of the protective antidote and poisoning of the cell. The antidote protein usually also exhibits an autoregulatory function of the operon. In this paper, we present the solution structure of ParD. The repressor activity of ParD is mediated by the N-terminal half of the protein, which adopts a ribbon-helix-helix (RHH) fold. The C-terminal half of the protein is unstructured in the absence of its cognate binding partner ParE. Based on homology with other RHH proteins, we present a model of the ParD-DNA interaction, with the antiparallel beta-strand being inserted into the major groove of DNA. The fusion of the N-terminal DNA-binding RHH motif to the toxin-binding unstructured C-terminal domain is discussed in its evolutionary context.
The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.,Oberer M, Zangger K, Gruber K, Keller W Protein Sci. 2007 Aug;16(8):1676-88. PMID:17656583[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Jiang Y, Pogliano J, Helinski DR, Konieczny I. ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase. Mol Microbiol. 2002 May;44(4):971-9. PMID:12010492
- ↑ Roberts RC, Helinski DR. Definition of a minimal plasmid stabilization system from the broad-host-range plasmid RK2. J Bacteriol. 1992 Dec;174(24):8119-32. PMID:1459960
- ↑ Roberts RC, Strom AR, Helinski DR. The parDE operon of the broad-host-range plasmid RK2 specifies growth inhibition associated with plasmid loss. J Mol Biol. 1994 Mar 18;237(1):35-51. PMID:8133518 doi:http://dx.doi.org/10.1006/jmbi.1994.1207
- ↑ Johnson EP, Strom AR, Helinski DR. Plasmid RK2 toxin protein ParE: purification and interaction with the ParD antitoxin protein. J Bacteriol. 1996 Mar;178(5):1420-9. PMID:8631720
- ↑ Oberer M, Zangger K, Gruber K, Keller W. The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding. Protein Sci. 2007 Aug;16(8):1676-88. PMID:17656583 doi:16/8/1676
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