2zle: Difference between revisions

Latest revision as of 13:57, 13 March 2024

Cryo-EM structure of DegP12/OMP

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Structural highlights

2zle is a 13 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 28Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DEGP_ECOLI DegP acts as a chaperone at low temperatures but switches to a peptidase (heat shock protein) at higher temperatures. It degrades transiently denatured and unfolded proteins which accumulate in the periplasm following heat shock or other stress conditions. DegP is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for beta-branched side chain amino acids. Only unfolded proteins devoid of disulfide bonds appear capable of being cleaved, thereby preventing non-specific proteolysis of folded proteins. Its proteolytic activity is essential for the survival of cells at elevated temperatures. It can degrade IciA, ada, casein, globin and PapA. DegP shares specificity with DegQ. DegP is also involved in the biogenesis of partially folded outer-membrane proteins (OMP).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Evolutionary Conservation

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

References

↑ Lipinska B, Zylicz M, Georgopoulos C. The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase. J Bacteriol. 1990 Apr;172(4):1791-7. PMID:2180903
↑ Kolmar H, Waller PR, Sauer RT. The DegP and DegQ periplasmic endoproteases of Escherichia coli: specificity for cleavage sites and substrate conformation. J Bacteriol. 1996 Oct;178(20):5925-9. PMID:8830688
↑ Spiess C, Beil A, Ehrmann M. A temperature-dependent switch from chaperone to protease in a widely conserved heat shock protein. Cell. 1999 Apr 30;97(3):339-47. PMID:10319814
↑ Krojer T, Pangerl K, Kurt J, Sawa J, Stingl C, Mechtler K, Huber R, Ehrmann M, Clausen T. Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins. Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7702-7. doi:, 10.1073/pnas.0803392105. Epub 2008 May 27. PMID:18505836 doi:10.1073/pnas.0803392105
↑ Pan KL, Hsiao HC, Weng CL, Wu MS, Chou CP. Roles of DegP in prevention of protein misfolding in the periplasm upon overexpression of penicillin acylase in Escherichia coli. J Bacteriol. 2003 May;185(10):3020-30. PMID:12730160
↑ Krojer T, Sawa J, Schafer E, Saibil HR, Ehrmann M, Clausen T. Structural basis for the regulated protease and chaperone function of DegP. Nature. 2008 Jun 12;453(7197):885-90. Epub 2008 May 21. PMID:18496527 doi:10.1038/nature07004

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OCA

[1] Lipinska B, Zylicz M, Georgopoulos C. The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase. J Bacteriol. 1990 Apr;172(4):1791-7. PMID:2180903

[2] Kolmar H, Waller PR, Sauer RT. The DegP and DegQ periplasmic endoproteases of Escherichia coli: specificity for cleavage sites and substrate conformation. J Bacteriol. 1996 Oct;178(20):5925-9. PMID:8830688

[3] Spiess C, Beil A, Ehrmann M. A temperature-dependent switch from chaperone to protease in a widely conserved heat shock protein. Cell. 1999 Apr 30;97(3):339-47. PMID:10319814

[4] Krojer T, Pangerl K, Kurt J, Sawa J, Stingl C, Mechtler K, Huber R, Ehrmann M, Clausen T. Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins. Proc Natl Acad Sci U S A. 2008 Jun 3;105(22):7702-7. doi:, 10.1073/pnas.0803392105. Epub 2008 May 27. PMID:18505836 doi:10.1073/pnas.0803392105

[5] Pan KL, Hsiao HC, Weng CL, Wu MS, Chou CP. Roles of DegP in prevention of protein misfolding in the periplasm upon overexpression of penicillin acylase in Escherichia coli. J Bacteriol. 2003 May;185(10):3020-30. PMID:12730160

[6] Krojer T, Sawa J, Schafer E, Saibil HR, Ehrmann M, Clausen T. Structural basis for the regulated protease and chaperone function of DegP. Nature. 2008 Jun 12;453(7197):885-90. Epub 2008 May 21. PMID:18496527 doi:10.1038/nature07004

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[2]

[3]

[4]

[5]

[6]

@@ Line 3: / Line 3: @@
 <SX load='2zle' size='340' side='right' viewer='molstar' caption='[[2zle]], [[Resolution|resolution]] 28.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zle]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZLE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zle]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZLE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZLE FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">degP, htrA, ptd ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), ompC, meoA, par ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 28&#8491;</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=2zle FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zle OCA], [https://pdbe.org/2zle PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zle RCSB], [https://www.ebi.ac.uk/pdbsum/2zle PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zle ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DEGP_ECOLI DEGP_ECOLI]] DegP acts as a chaperone at low temperatures but switches to a peptidase (heat shock protein) at higher temperatures. It degrades transiently denatured and unfolded proteins which accumulate in the periplasm following heat shock or other stress conditions. DegP is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for beta-branched side chain amino acids. Only unfolded proteins devoid of disulfide bonds appear capable of being cleaved, thereby preventing non-specific proteolysis of folded proteins. Its proteolytic activity is essential for the survival of cells at elevated temperatures. It can degrade IciA, ada, casein, globin and PapA. DegP shares specificity with DegQ. DegP is also involved in the biogenesis of partially folded outer-membrane proteins (OMP).<ref>PMID:2180903</ref> <ref>PMID:8830688</ref> <ref>PMID:10319814</ref> <ref>PMID:18505836</ref> <ref>PMID:12730160</ref> <ref>PMID:18496527</ref>  [[https://www.uniprot.org/uniprot/OMPC_ECOLI OMPC_ECOLI]] Forms pores that allow passive diffusion of small molecules across the outer membrane.
+[https://www.uniprot.org/uniprot/DEGP_ECOLI DEGP_ECOLI] DegP acts as a chaperone at low temperatures but switches to a peptidase (heat shock protein) at higher temperatures. It degrades transiently denatured and unfolded proteins which accumulate in the periplasm following heat shock or other stress conditions. DegP is efficient with Val-Xaa and Ile-Xaa peptide bonds, suggesting a preference for beta-branched side chain amino acids. Only unfolded proteins devoid of disulfide bonds appear capable of being cleaved, thereby preventing non-specific proteolysis of folded proteins. Its proteolytic activity is essential for the survival of cells at elevated temperatures. It can degrade IciA, ada, casein, globin and PapA. DegP shares specificity with DegQ. DegP is also involved in the biogenesis of partially folded outer-membrane proteins (OMP).<ref>PMID:2180903</ref> <ref>PMID:8830688</ref> <ref>PMID:10319814</ref> <ref>PMID:18505836</ref> <ref>PMID:12730160</ref> <ref>PMID:18496527</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / Line 19: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2zle ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases.
-Structural basis for the regulated protease and chaperone function of DegP.,Krojer T, Sawa J, Schafer E, Saibil HR, Ehrmann M, Clausen T Nature. 2008 Jun 12;453(7197):885-90. Epub 2008 May 21. PMID:18496527<ref>PMID:18496527</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2zle" style="background-color:#fffaf0;"></div>
 ==See Also==
+*[[Heat Shock Protein structures|Heat Shock Protein structures]]
 *[[Porin 3D structures|Porin 3D structures]]
 == References ==
@@ Line 35: / Line 27: @@
 __TOC__
 </SX>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Saibil, H R]]
+[[Category: Saibil HR]]
-[[Category: Schaefer, E]]
+[[Category: Schaefer E]]
-[[Category: Chaperone]]
-[[Category: Degp]]
-[[Category: Htra]]
-[[Category: Hydrolase]]
-[[Category: Ion transport]]
-[[Category: Omp]]
-[[Category: Outer membrane protein]]
-[[Category: Pdz]]
-[[Category: Periplasm]]
-[[Category: Phage recognition]]
-[[Category: Porin]]
-[[Category: Protease]]
-[[Category: Serine protease]]
-[[Category: Stress response]]
-[[Category: Transmembrane]]
-[[Category: Transport]]

2zle: Difference between revisions

Latest revision as of 13:57, 13 March 2024

Cryo-EM structure of DegP12/OMP

Structural highlights

Function

Evolutionary Conservation

See Also

References

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