1rre

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of E.coli Lon proteolytic domain

Structural highlights

1rre is a 6 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:	X-ray diffraction, Resolution 1.75Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LON_ECOLI ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins, including some antitoxins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner. Endogenous substrates include the regulatory proteins RcsA and SulA, the transcriptional activator SoxS, and UmuD. Its overproduction specifically inhibits translation through at least two different pathways, one of them being the YoeB-YefM toxin-antitoxin system.^[1] ^[2] ^[3]

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

ATP-dependent Lon protease degrades specific short-lived regulatory proteins as well as defective and abnormal proteins in the cell. The crystal structure of the proteolytic domain (P domain) of the Escherichia coli Lon has been solved by single-wavelength anomalous dispersion and refined at 1.75-A resolution. The P domain was obtained by chymotrypsin digestion of the full-length, proteolytically inactive Lon mutant (S679A) or by expression of a recombinant construct encoding only this domain. The P domain has a unique fold and assembles into hexameric rings that likely mimic the oligomerization state of the holoenzyme. The hexamer is dome-shaped, with the six N termini oriented toward the narrower ring surface, which is thus identified as the interface with the ATPase domain in full-length Lon. The catalytic sites lie in a shallow concavity on the wider distal surface of the hexameric ring and are connected to the proximal surface by a narrow axial channel with a diameter of approximately 18 A. Within the active site, the proximity of Lys(722) to the side chain of the mutated Ala(679) and the absence of other potential catalytic side chains establish that Lon employs a Ser(679)-Lys(722) dyad for catalysis. Alignment of the P domain catalytic pocket with those of several Ser-Lys dyad peptide hydrolases provides a model of substrate binding, suggesting that polypeptides are oriented in the Lon active site to allow nucleophilic attack by the serine hydroxyl on the si-face of the peptide bond.

The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.,Botos I, Melnikov EE, Cherry S, Tropea JE, Khalatova AG, Rasulova F, Dauter Z, Maurizi MR, Rotanova TV, Wlodawer A, Gustchina A J Biol Chem. 2004 Feb 27;279(9):8140-8. Epub 2003 Dec 9. PMID:14665623^[4]

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

References

↑ Thomas-Wohlever J, Lee I. Kinetic characterization of the peptidase activity of Escherichia coli Lon reveals the mechanistic similarities in ATP-dependent hydrolysis of peptide and protein substrates. Biochemistry. 2002 Jul 30;41(30):9418-25. PMID:12135363
↑ Vineyard D, Patterson-Ward J, Lee I. Single-turnover kinetic experiments confirm the existence of high- and low-affinity ATPase sites in Escherichia coli Lon protease. Biochemistry. 2006 Apr 11;45(14):4602-10. PMID:16584195 doi:10.1021/bi052377t
↑ Duval V, Nicoloff H, Levy SB. Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli. Antimicrob Agents Chemother. 2009 Nov;53(11):4944-8. doi: 10.1128/AAC.00787-09., Epub 2009 Aug 31. PMID:19721064 doi:10.1128/AAC.00787-09
↑ Botos I, Melnikov EE, Cherry S, Tropea JE, Khalatova AG, Rasulova F, Dauter Z, Maurizi MR, Rotanova TV, Wlodawer A, Gustchina A. The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J Biol Chem. 2004 Feb 27;279(9):8140-8. Epub 2003 Dec 9. PMID:14665623 doi:http://dx.doi.org/10.1074/jbc.M312243200

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1rre"

@@ Line 1: / Line 1: @@
 ==Crystal structure of E.coli Lon proteolytic domain==
-<StructureSection load='1rre' size='340' side='right' caption='[[1rre]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='1rre' size='340' side='right'caption='[[1rre]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rre]] is a 6 chain structure with 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=1RRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RRE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rre]] is a 6 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=1RRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RRE FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1rr9|1rr9]]</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=1rre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rre OCA], [https://pdbe.org/1rre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rre RCSB], [https://www.ebi.ac.uk/pdbsum/1rre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rre ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LON, CAPR, DEG, MUC, LOPA, B0439, C0555 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
+</table>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endopeptidase_La Endopeptidase La], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.53 3.4.21.53] </span></td></tr>
+== Function ==
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rre OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rre RCSB], [http://www.ebi.ac.uk/pdbsum/1rre PDBsum]</span></td></tr>
+[https://www.uniprot.org/uniprot/LON_ECOLI LON_ECOLI] ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins, including some antitoxins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner. Endogenous substrates include the regulatory proteins RcsA and SulA, the transcriptional activator SoxS, and UmuD. Its overproduction specifically inhibits translation through at least two different pathways, one of them being the YoeB-YefM toxin-antitoxin system.<ref>PMID:12135363</ref> <ref>PMID:16584195</ref> <ref>PMID:19721064</ref>
-<table>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rr/1rre_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rr/1rre_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1rre ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1rre" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Endopeptidase La]]
 [[Category: Escherichia coli]]
-[[Category: Botos, I.]]
+[[Category: Large Structures]]
-[[Category: Cherry, S.]]
+[[Category: Botos I]]
-[[Category: Dauter, Z.]]
+[[Category: Cherry S]]
-[[Category: Gustchina, A.]]
+[[Category: Dauter Z]]
-[[Category: Khalatova, A G.]]
+[[Category: Gustchina A]]
-[[Category: Maurizi, M R.]]
+[[Category: Khalatova AG]]
-[[Category: Melnikov, E E.]]
+[[Category: Maurizi MR]]
-[[Category: Rasulova, F.]]
+[[Category: Melnikov EE]]
-[[Category: Rotanova, T V.]]
+[[Category: Rasulova F]]
-[[Category: Tropea, J E.]]
+[[Category: Rotanova TV]]
-[[Category: Wlodawer, A.]]
+[[Category: Tropea JE]]
-[[Category: Atp-dependent protease]]
+[[Category: Wlodawer A]]
-[[Category: Catalytic ser-lys dyad]]
-[[Category: Hydrolase]]

1rre

From Proteopedia

Current revision

Crystal structure of E.coli Lon proteolytic domain

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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