2w9r

From Proteopedia

(Difference between revisions)

Revision as of 11:01, 6 April 2022

Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS

Structural highlights

2w9r is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1lzw, 1mbu, 1jre, 1l8h, 1mg9, 1mbv, 1l8i, 1r6o, 1jts, 1f33, 1f30, 1r6q, 1mbx, 1dps
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CLPS_ECOLI] Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. [DPS_ECOLI] During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.^[1] ^[2] ^[3] ^[4]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

In Escherichia coli, the ClpAP protease, together with the adaptor protein ClpS, is responsible for the degradation of proteins bearing an amino-terminal destabilizing amino acid (N-degron). Here, we determined the three-dimensional structures of ClpS in complex with three peptides, each having a different destabilizing residue--Leu, Phe or Trp--at its N terminus. All peptides, regardless of the identity of their N-terminal residue, are bound in a surface pocket on ClpS in a stereo-specific manner. Several highly conserved residues in this binding pocket interact directly with the backbone of the N-degron peptide and hence are crucial for the binding of all N-degrons. By contrast, two hydrophobic residues define the volume of the binding pocket and influence the specificity of ClpS. Taken together, our data suggest that ClpS has been optimized for the binding and delivery of N-degrons containing an N-terminal Phe or Leu.

Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS.,Schuenemann VJ, Kralik SM, Albrecht R, Spall SK, Truscott KN, Dougan DA, Zeth K EMBO Rep. 2009 May;10(5):508-14. Epub 2009 Apr 17. PMID:19373253^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Almiron M, Link AJ, Furlong D, Kolter R. A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 1992 Dec;6(12B):2646-54. PMID:1340475
↑ Wolf SG, Frenkiel D, Arad T, Finkel SE, Kolter R, Minsky A. DNA protection by stress-induced biocrystallization. Nature. 1999 Jul 1;400(6739):83-5. PMID:10403254 doi:http://dx.doi.org/10.1038/21918
↑ Nair S, Finkel SE. Dps protects cells against multiple stresses during stationary phase. J Bacteriol. 2004 Jul;186(13):4192-8. PMID:15205421 doi:http://dx.doi.org/10.1128/JB.186.13.4192-4198.2004
↑ Ceci P, Cellai S, Falvo E, Rivetti C, Rossi GL, Chiancone E. DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res. 2004 Nov 8;32(19):5935-44. Print 2004. PMID:15534364 doi:http://dx.doi.org/32/19/5935
↑ Schuenemann VJ, Kralik SM, Albrecht R, Spall SK, Truscott KN, Dougan DA, Zeth K. Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS. EMBO Rep. 2009 May;10(5):508-14. Epub 2009 Apr 17. PMID:19373253 doi:10.1038/embor.2009.62

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2w9r"

@@ Line 3: / Line 3: @@
 <StructureSection load='2w9r' size='340' side='right'caption='[[2w9r]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2w9r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W9R OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2W9R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2w9r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W9R FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1lzw|1lzw]], [[1mbu|1mbu]], [[1jre|1jre]], [[1l8h|1l8h]], [[1mg9|1mg9]], [[1mbv|1mbv]], [[1l8i|1l8i]], [[1r6o|1r6o]], [[1jts|1jts]], [[1f33|1f33]], [[1f30|1f30]], [[1r6q|1r6q]], [[1mbx|1mbx]], [[1dps|1dps]]</td></tr>
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lzw|1lzw]], [[1mbu|1mbu]], [[1jre|1jre]], [[1l8h|1l8h]], [[1mg9|1mg9]], [[1mbv|1mbv]], [[1l8i|1l8i]], [[1r6o|1r6o]], [[1jts|1jts]], [[1f33|1f33]], [[1f30|1f30]], [[1r6q|1r6q]], [[1mbx|1mbx]], [[1dps|1dps]]</div></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2w9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w9r OCA], [http://pdbe.org/2w9r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w9r RCSB], [http://www.ebi.ac.uk/pdbsum/2w9r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w9r ProSAT]</span></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=2w9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w9r OCA], [https://pdbe.org/2w9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w9r RCSB], [https://www.ebi.ac.uk/pdbsum/2w9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w9r ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CLPS_ECOLI CLPS_ECOLI]] Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. [[http://www.uniprot.org/uniprot/DPS_ECOLI DPS_ECOLI]] During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.<ref>PMID:1340475</ref> <ref>PMID:10403254</ref> <ref>PMID:15205421</ref> <ref>PMID:15534364</ref>
+[[https://www.uniprot.org/uniprot/CLPS_ECOLI CLPS_ECOLI]] Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation. [[https://www.uniprot.org/uniprot/DPS_ECOLI DPS_ECOLI]] During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.<ref>PMID:1340475</ref> <ref>PMID:10403254</ref> <ref>PMID:15205421</ref> <ref>PMID:15534364</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

2w9r

From Proteopedia

Revision as of 11:01, 6 April 2022

Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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