3k0t: Difference between revisions

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[[Image:3k0t.jpg|left|200px]]


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==Crystal structure of PSPTO -PSP protein in complex with D-beta-Glucose from Pseudomonas syringae pv. tomato str. DC3000==
The line below this paragraph, containing "STRUCTURE_3k0t", creates the "Structure Box" on the page.
<StructureSection load='3k0t' size='340' side='right'caption='[[3k0t]], [[Resolution|resolution]] 2.10&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'>[[3k0t]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_syringae_pv._tomato Pseudomonas syringae pv. tomato]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K0T FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_3k0t|  PDB=3k0t  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3k0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k0t OCA], [https://pdbe.org/3k0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k0t RCSB], [https://www.ebi.ac.uk/pdbsum/3k0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k0t ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q88BE5_PSESM Q88BE5_PSESM]
== 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/k0/3k0t_consurf.spt"</scriptWhenChecked>
    <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/main_output.php?pdb_ID=3k0t ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The perchloric acid-soluble protein (PSP) is an endoribonuclease and on the basis of sequence similarity has been assigned to the YjgF/YER057c/UK114 family. These family members are ubiquitous and highly conserved in evolution, and participate in regulating basic cellular metabolism. Here we present the 2.1A crystal structure of the PSP protein from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO-PSP), in complex with D-glucose. The quaternary structure of PSPTO-PSP is a homologous trimer. Glucose is located in the cavity between each two monomers. Comparison of the hydrogen bonds between ligands and YjgF/YER057c/UK114 family homologues confirms that the conserved Arg(103) of PSPTO-PSP is a key amino acid in this cavity for ligand binding. It indicated that the involvement of PSPTO-PSP in essential cellular mechanism was regulated by glucose occupying this active site.


===Crystal structure of PSPTO -PSP protein in complex with D-beta-Glucose from Pseudomonas syringae pv. tomato str. DC3000===
Crystal structure of the PSPTO-PSP protein from Pseudomonas syringae pv. tomato str. DC3000 in complex with D-glucose.,Zhang HM, Gao Y, Li M, Chang WR Biochem Biophys Res Commun. 2010 Jun 18;397(1):82-6. Epub 2010 May 15. PMID:20478270<ref>PMID:20478270</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_20478270}}, adds the Publication Abstract to the page
<div class="pdbe-citations 3k0t" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20478270 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20478270}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3K0T is a 3 chains structure with sequences from [http://en.wikipedia.org/wiki/Pseudomonas_syringae_pv._tomato Pseudomonas syringae pv. tomato]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K0T OCA].
 
==Reference==
<ref group="xtra">PMID:20478270</ref><references group="xtra"/>
[[Category: Pseudomonas syringae pv. tomato]]
[[Category: Pseudomonas syringae pv. tomato]]
[[Category: Chang, W R.]]
[[Category: Chang WR]]
[[Category: Li, M.]]
[[Category: Li M]]
[[Category: Zhang, H M.]]
[[Category: Zhang HM]]
[[Category: Er stressor]]
[[Category: Glucose binding]]
[[Category: Psp]]
[[Category: Sugar binding protein]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:38:34 2010''

Latest revision as of 13:03, 6 November 2024

Crystal structure of PSPTO -PSP protein in complex with D-beta-Glucose from Pseudomonas syringae pv. tomato str. DC3000Crystal structure of PSPTO -PSP protein in complex with D-beta-Glucose from Pseudomonas syringae pv. tomato str. DC3000

Structural highlights

3k0t is a 3 chain structure with sequence from Pseudomonas syringae pv. tomato. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q88BE5_PSESM

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 perchloric acid-soluble protein (PSP) is an endoribonuclease and on the basis of sequence similarity has been assigned to the YjgF/YER057c/UK114 family. These family members are ubiquitous and highly conserved in evolution, and participate in regulating basic cellular metabolism. Here we present the 2.1A crystal structure of the PSP protein from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO-PSP), in complex with D-glucose. The quaternary structure of PSPTO-PSP is a homologous trimer. Glucose is located in the cavity between each two monomers. Comparison of the hydrogen bonds between ligands and YjgF/YER057c/UK114 family homologues confirms that the conserved Arg(103) of PSPTO-PSP is a key amino acid in this cavity for ligand binding. It indicated that the involvement of PSPTO-PSP in essential cellular mechanism was regulated by glucose occupying this active site.

Crystal structure of the PSPTO-PSP protein from Pseudomonas syringae pv. tomato str. DC3000 in complex with D-glucose.,Zhang HM, Gao Y, Li M, Chang WR Biochem Biophys Res Commun. 2010 Jun 18;397(1):82-6. Epub 2010 May 15. PMID:20478270[1]

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

References

  1. ↑ Zhang HM, Gao Y, Li M, Chang WR. Crystal structure of the PSPTO-PSP protein from Pseudomonas syringae pv. tomato str. DC3000 in complex with D-glucose. Biochem Biophys Res Commun. 2010 Jun 18;397(1):82-6. Epub 2010 May 15. PMID:20478270 doi:10.1016/j.bbrc.2010.05.071

3k0t, resolution 2.10Å

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