2qmi: Difference between revisions

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==Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi==
==Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi==
<StructureSection load='2qmi' size='340' side='right' caption='[[2qmi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='2qmi' size='340' side='right'caption='[[2qmi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2qmi]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QMI FirstGlance]. <br>
<table><tr><td colspan='2'>[[2qmi]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QMI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DO3:10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE+1,4,7-TRIACETIC+ACID'>DO3</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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]] 2.2&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pbp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 Pyrococcus abyssi])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DO3:10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE+1,4,7-TRIACETIC+ACID'>DO3</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span></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=2qmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qmi OCA], [https://pdbe.org/2qmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qmi RCSB], [https://www.ebi.ac.uk/pdbsum/2qmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qmi ProSAT]</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=2qmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qmi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qmi RCSB], [http://www.ebi.ac.uk/pdbsum/2qmi PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9V2D6_PYRAB Q9V2D6_PYRAB]
== 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/qm/2qmi_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qm/2qmi_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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=2qmi ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.
Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.,Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C PLoS One. 2009;4(3):e4712. Epub 2009 Mar 5. PMID:19266066<ref>PMID:19266066</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Beta-lactamase]]
[[Category: Large Structures]]
[[Category: Pyrococcus abyssi]]
[[Category: Pyrococcus abyssi]]
[[Category: Delfosse, V]]
[[Category: Delfosse V]]
[[Category: Girard, E]]
[[Category: Girard E]]
[[Category: Mayer, C]]
[[Category: Mayer C]]
[[Category: Moulinier, L]]
[[Category: Moulinier L]]
[[Category: Schultz, P]]
[[Category: Schultz P]]
[[Category: Archaea]]
[[Category: Hydrolase]]
[[Category: Lu-hpdo3a]]
[[Category: Octamer]]
[[Category: Pab87]]
[[Category: Pbp]]

Latest revision as of 12:16, 21 February 2024

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssiStructure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

Structural highlights

2qmi is a 8 chain structure with sequence from Pyrococcus abyssi. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9V2D6_PYRAB

Evolutionary Conservation

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

2qmi, resolution 2.20Å

Drag the structure with the mouse to rotate

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OCA
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