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3o2h

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Revision as of 07:14, 12 May 2022

E. coli ClpS in complex with a Leu N-end rule peptide

Structural highlights

3o2h 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:	2w9r, 3o1f, 3o2o
Gene:	clpS (ECOLI)
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]

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 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3o2h"

@@ Line 1: / Line 1: @@
 ==E. coli ClpS in complex with a Leu N-end rule peptide==
-<StructureSection load='3o2h' size='340' side='right' caption='[[3o2h]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+<StructureSection load='3o2h' size='340' side='right'caption='[[3o2h]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3o2h]] 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=3O2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3O2H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3o2h]] 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=3O2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3O2H FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2w9r|2w9r]], [[3o1f|3o1f]], [[3o2o|3o2o]]</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;'>[[2w9r|2w9r]], [[3o1f|3o1f]], [[3o2o|3o2o]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clpS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clpS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3o2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o2h OCA], [http://pdbe.org/3o2h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3o2h RCSB], [http://www.ebi.ac.uk/pdbsum/3o2h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3o2h 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=3o2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3o2h OCA], [https://pdbe.org/3o2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3o2h RCSB], [https://www.ebi.ac.uk/pdbsum/3o2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3o2h 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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 ==See Also==
 *[[ATP-dependent Clp protease adaptor protein|ATP-dependent Clp protease adaptor protein]]
+*[[ATP-dependent Clp protease adaptor protein 3D structures|ATP-dependent Clp protease adaptor protein 3D structures]]
 == References ==
 <references/>
@@ Line 27: / Line 28: @@
 </StructureSection>
 [[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Baker, T A]]
 [[Category: Grant, R A]]

3o2h

From Proteopedia

Revision as of 07:14, 12 May 2022

E. coli ClpS in complex with a Leu N-end rule peptide

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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