2zpm: Difference between revisions

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{{Seed}}
[[Image:2zpm.png|left|200px]]


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==Crystal structure analysis of PDZ domain B==
The line below this paragraph, containing "STRUCTURE_2zpm", creates the "Structure Box" on the page.
<StructureSection load='2zpm' size='340' side='right'caption='[[2zpm]], [[Resolution|resolution]] 0.98&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2zpm]] is a 1 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=2ZPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZPM FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2zpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zpm OCA], [https://pdbe.org/2zpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zpm RCSB], [https://www.ebi.ac.uk/pdbsum/2zpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zpm ProSAT]</span></td></tr>
{{STRUCTURE_2zpm|  PDB=2zpm  |  SCENE=  }}
</table>
 
== Function ==
===Crystal structure analysis of PDZ domain B===
[[https://www.uniprot.org/uniprot/RSEP_ECOLI RSEP_ECOLI]] A site-2 regulated intramembrane protease (S2P) that cleaves the peptide bond between 'Ala-108' and 'Cys-109' in the transmembrane region of RseA. Part of a regulated intramembrane proteolysis (RIP) cascade. Acts on DegS-cleaved RseA to release the cytoplasmic domain of RseA, residue "Val-148" of RseA may be required for this. This provides the cell with sigma-E (RpoE) activity through the proteolysis of RseA. Can also cleave sequences in transmembrane regions of other proteins (such as LacY) as well as liberated signal peptides of beta-lactamase, OmpF, LivK, SecM, PhoA, LivJ, OmpC, Lpp and TorA, probably within the membrane.<ref>PMID:11750129</ref> <ref>PMID:12183368</ref> <ref>PMID:12183369</ref> <ref>PMID:15496982</ref> <ref>PMID:18268014</ref> <ref>PMID:21810987</ref> <ref>PMID:18945679</ref> 
 
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
==About this Structure==
Check<jmol>
2ZPM is a 1 chain structure of 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=2ZPM OCA].  
  <jmolCheckbox>
[[Category: Escherichia coli]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zp/2zpm_consurf.spt"</scriptWhenChecked>
[[Category: Inaba, K.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Suzuki, M.]]
    <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/main_output.php?pdb_ID=2zpm ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Ecoli]]
[[Category: Large Structures]]
[[Category: Inaba, K]]
[[Category: Suzuki, M]]
[[Category: Hydrolase]]
[[Category: Hydrolase]]
[[Category: Inner membrane]]
[[Category: Inner membrane]]
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[[Category: Transmembrane]]
[[Category: Transmembrane]]
[[Category: Zinc]]
[[Category: Zinc]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:37:08 2009''

Latest revision as of 20:35, 15 December 2021

Crystal structure analysis of PDZ domain BCrystal structure analysis of PDZ domain B

Structural highlights

2zpm is a 1 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RSEP_ECOLI] A site-2 regulated intramembrane protease (S2P) that cleaves the peptide bond between 'Ala-108' and 'Cys-109' in the transmembrane region of RseA. Part of a regulated intramembrane proteolysis (RIP) cascade. Acts on DegS-cleaved RseA to release the cytoplasmic domain of RseA, residue "Val-148" of RseA may be required for this. This provides the cell with sigma-E (RpoE) activity through the proteolysis of RseA. Can also cleave sequences in transmembrane regions of other proteins (such as LacY) as well as liberated signal peptides of beta-lactamase, OmpF, LivK, SecM, PhoA, LivJ, OmpC, Lpp and TorA, probably within the membrane.[1] [2] [3] [4] [5] [6] [7]

Evolutionary Conservation

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

References

  1. ↑ Kanehara K, Akiyama Y, Ito K. Characterization of the yaeL gene product and its S2P-protease motifs in Escherichia coli. Gene. 2001 Dec 27;281(1-2):71-9. PMID:11750129
  2. ↑ Kanehara K, Ito K, Akiyama Y. YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA. Genes Dev. 2002 Aug 15;16(16):2147-55. PMID:12183368 doi:http://dx.doi.org/10.1101/gad.1002302
  3. ↑ Alba BM, Leeds JA, Onufryk C, Lu CZ, Gross CA. DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response. Genes Dev. 2002 Aug 15;16(16):2156-68. PMID:12183369 doi:10.1101/gad.1008902
  4. ↑ Akiyama Y, Kanehara K, Ito K. RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences. EMBO J. 2004 Nov 10;23(22):4434-42. Epub 2004 Oct 21. PMID:15496982 doi:http://dx.doi.org/7600449
  5. ↑ Koide K, Ito K, Akiyama Y. Substrate recognition and binding by RseP, an Escherichia coli intramembrane protease. J Biol Chem. 2008 Apr 11;283(15):9562-70. doi: 10.1074/jbc.M709984200. Epub 2008 , Feb 11. PMID:18268014 doi:http://dx.doi.org/10.1074/jbc.M709984200
  6. ↑ Saito A, Hizukuri Y, Matsuo E, Chiba S, Mori H, Nishimura O, Ito K, Akiyama Y. Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13740-5. doi:, 10.1073/pnas.1108376108. Epub 2011 Aug 2. PMID:21810987 doi:http://dx.doi.org/10.1073/pnas.1108376108
  7. ↑ Inaba K, Suzuki M, Maegawa K, Akiyama S, Ito K, Akiyama Y. A pair of circularly permutated PDZ domains control RseP, the S2P family intramembrane protease of Escherichia coli. J Biol Chem. 2008 Dec 12;283(50):35042-52. doi: 10.1074/jbc.M806603200. Epub 2008, Oct 22. PMID:18945679 doi:http://dx.doi.org/10.1074/jbc.M806603200

2zpm, resolution 0.98Å

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