|
|
| Line 1: |
Line 1: |
| | | | |
| | ==Crystal structure of Lon N-terminal domain.== | | ==Crystal structure of Lon N-terminal domain.== |
| - | <StructureSection load='3ljc' size='340' side='right' caption='[[3ljc]], [[Resolution|resolution]] 2.60Å' scene=''> | + | <StructureSection load='3ljc' size='340' side='right'caption='[[3ljc]], [[Resolution|resolution]] 2.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ljc]] is a 1 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=3LJC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LJC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ljc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LJC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LJC FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ane|2ane]]</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></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lon, capR, deg, lopA, muc, b0439, JW0429 ([http://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'>[https://proteopedia.org/fgij/fg.htm?mol=3ljc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ljc OCA], [https://pdbe.org/3ljc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ljc RCSB], [https://www.ebi.ac.uk/pdbsum/3ljc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ljc ProSAT]</span></td></tr> |
| - | <tr id='activity'><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>
| + | |
| - | <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=3ljc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ljc OCA], [http://pdbe.org/3ljc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ljc RCSB], [http://www.ebi.ac.uk/pdbsum/3ljc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ljc ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/3ljc_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/3ljc_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> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
| Line 35: |
Line 33: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| - | [[Category: Endopeptidase La]] | + | [[Category: Large Structures]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter Z]] |
| - | [[Category: Gustchina, A]] | + | [[Category: Gustchina A]] |
| - | [[Category: Li, M]] | + | [[Category: Li M]] |
| - | [[Category: Wlodawer, A]] | + | [[Category: Wlodawer A]] |
| - | [[Category: Allosteric enzyme]]
| + | |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Dna-binding]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lon n-domain]]
| + | |
| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Protease]]
| + | |
| - | [[Category: Serine protease]]
| + | |
| - | [[Category: Stress response]]
| + | |
| Structural highlights
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
The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 A resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal alpha-helix. The structure of the first subdomain (residues 1-117), which consists mostly of beta-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas the second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.
Structure of the N-terminal fragment of Escherichia coli Lon protease.,Li M, Gustchina A, Rasulova FS, Melnikov EE, Maurizi MR, Rotanova TV, Dauter Z, Wlodawer A Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):865-73. Epub 2010, Jul 9. PMID:20693685[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
- ↑ Li M, Gustchina A, Rasulova FS, Melnikov EE, Maurizi MR, Rotanova TV, Dauter Z, Wlodawer A. Structure of the N-terminal fragment of Escherichia coli Lon protease. Acta Crystallogr D Biol Crystallogr. 2010 Aug;66(Pt 8):865-73. Epub 2010, Jul 9. PMID:20693685 doi:10.1107/S0907444910019554
|
