3ktk

From Proteopedia

(Difference between revisions)

Revision as of 07:10, 2 January 2019

Structure of ClpP in complex with ADEP2 in triclinic crystal form

Structural highlights

3ktk is a 28 chain structure with sequence from "vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:	, , , , ,
Related:	3ktg, 3kth, 3kti, 3ktj
Gene:	clpP, yvdN, BSU34540 ("Vibrio subtilis" Ehrenberg 1835)
Activity:	Endopeptidase Clp, with EC number 3.4.21.92
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CLPP_BACSU] Cleaves peptides in various proteins in a process that requires ATP hydrolysis. Has a chymotrypsin-like activity. Plays a major role in the degradation of misfolded proteins (By similarity). ClpXP is involved in the complete degradation of the Site-2 clipped anti-sigma-W factor RsiW. This results in the release of SigW and the transcription activation of the genes under the control of the sigma-W factor.^[1]

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

Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. Nonetheless, the proteolytic activation mechanism has remained elusive because of the lack of a complex structure. Acyldepsipeptides (ADEPs), a recently discovered class of antibiotics, activate and disregulate ClpP. Here we have elucidated the structural changes underlying the ClpP activation process by ADEPs. We present the structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2. The structures show the closed-to-open-gate transition of the ClpP N-terminal segments upon activation as well as conformational changes restricted to the upper portion of ClpP. The direction of the conformational movement and the hydrophobic clustering that stabilizes the closed structure are markedly different from those of other ATP-dependent proteases, providing unprecedented insights into the activation of ClpP.

Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.,Lee BG, Park EY, Lee KE, Jeon H, Sung KH, Paulsen H, Rubsamen-Schaeff H, Brotz-Oesterhelt H, Song HK Nat Struct Mol Biol. 2010 Apr;17(4):471-8. Epub 2010 Mar 21. PMID:20305655^[2]

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

References

↑ Zellmeier S, Schumann W, Wiegert T. Involvement of Clp protease activity in modulating the Bacillus subtilissigmaw stress response. Mol Microbiol. 2006 Sep;61(6):1569-82. Epub 2006 Aug 8. PMID:16899079 doi:MMI5323
↑ Lee BG, Park EY, Lee KE, Jeon H, Sung KH, Paulsen H, Rubsamen-Schaeff H, Brotz-Oesterhelt H, Song HK. Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat Struct Mol Biol. 2010 Apr;17(4):471-8. Epub 2010 Mar 21. PMID:20305655 doi:10.1038/nsmb.1787

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/3ktk"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ktk' size='340' side='right' caption='[[3ktk]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ktk]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KTK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ktk]] is a 28 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KTK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KTK FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXP:CYCLOHEXANE+PROPIONIC+ACID'>CXP</scene>, <scene name='pdbligand=MP8:(4R)-4-METHYL-L-PROLINE'>MP8</scene>, <scene name='pdbligand=WFP:3,5-DIFLUORO-L-PHENYLALANINE'>WFP</scene>, <scene name='pdbligand=YCP:(2S)-PIPERIDINE-2-CARBOXYLIC+ACID'>YCP</scene></td></tr>
+</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXP:CYCLOHEXANE+PROPIONIC+ACID'>CXP</scene>, <scene name='pdbligand=MAA:N-METHYL-L-ALANINE'>MAA</scene>, <scene name='pdbligand=MP8:(4R)-4-METHYL-L-PROLINE'>MP8</scene>, <scene name='pdbligand=OTT:(2E,4E,6E)-OCTA-2,4,6-TRIENOIC+ACID'>OTT</scene>, <scene name='pdbligand=WFP:3,5-DIFLUORO-L-PHENYLALANINE'>WFP</scene>, <scene name='pdbligand=YCP:(2S)-PIPERIDINE-2-CARBOXYLIC+ACID'>YCP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ktg|3ktg]], [[3kth|3kth]], [[3kti|3kti]], [[3ktj|3ktj]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clpP, yvdN, BSU34540 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">clpP, yvdN, BSU34540 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_Clp Endopeptidase Clp], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.92 3.4.21.92] </span></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=3ktk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ktk OCA], [http://pdbe.org/3ktk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ktk RCSB], [http://www.ebi.ac.uk/pdbsum/3ktk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ktk ProSAT]</span></td></tr>
@@ Line 16: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kt/3ktk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kt/3ktk_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 38: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus globigii migula 1900]]
+[[Category: Vibrio subtilis ehrenberg 1835]]
 [[Category: Endopeptidase Clp]]
 [[Category: Brotz-Oesterhelt, H]]

3ktk

From Proteopedia

Revision as of 07:10, 2 January 2019

Structure of ClpP in complex with ADEP2 in triclinic crystal form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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