1e3h: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1e3h.jpg|left|200px]]


{{Structure
==SeMet derivative of Streptomyces antibioticus PNPase/GPSI enzyme==
|PDB= 1e3h |SIZE=350|CAPTION= <scene name='initialview01'>1e3h</scene>, resolution 2.60&Aring;
<StructureSection load='1e3h' size='340' side='right'caption='[[1e3h]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
<table><tr><td colspan='2'>[[1e3h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E3H FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
|GENE= GPSI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1890 Streptomyces antibioticus])
<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>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1e3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e3h OCA], [https://pdbe.org/1e3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e3h RCSB], [https://www.ebi.ac.uk/pdbsum/1e3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e3h ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1e3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e3h OCA], [http://www.ebi.ac.uk/pdbsum/1e3h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1e3h RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/PNP_STRAT PNP_STRAT] Involved in mRNA degradation. Catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction.[HAMAP-Rule:MF_01595]
== 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/e3/1e3h_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=1e3h ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
BACKGROUND: Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes. Streptomyces antibioticus PNPase also assays as a guanosine 3'-diphosphate 5'-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle. RESULTS: The structure of S. antibioticus PNPase without bound RNA but with the phosphate analog tungstate bound at the PNPase catalytic sites was determined by X-ray crystallography and shows a trimeric multidomain protein with a central channel. The structural core has a novel duplicated architecture formed by association of two homologous domains. The tungstate derivative structure reveals the PNPase active site in the second of these core domains. Structure-based sequence analysis suggests that the pppGpp synthetase active site is located in the first core domain. CONCLUSIONS: This is the first structure of a PNPase and shows the structural basis for the trimer assembly, the arrangement of accessory RNA binding domains, and the likely catalytic residues of the PNPase active site. A possible function of the trimer channel is as a contribution to both the processivity of degradation and the regulation of PNPase action by RNA structural elements.


'''SEMET DERIVATIVE OF STREPTOMYCES ANTIBIOTICUS PNPASE/GPSI ENZYME'''
A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation.,Symmons MF, Jones GH, Luisi BF Structure. 2000 Nov 15;8(11):1215-26. PMID:11080643<ref>PMID:11080643</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1e3h" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
BACKGROUND: Polynucleotide phosphorylase (PNPase) is a polyribonucleotide nucleotidyl transferase (E.C.2.7.7.8) that degrades mRNA in prokaryotes. Streptomyces antibioticus PNPase also assays as a guanosine 3'-diphosphate 5'-triphosphate (pppGpp) synthetase (E.C.2.7.6.5). It may function to coordinate changes in mRNA lifetimes with pppGpp levels during the Streptomyces lifecycle. RESULTS: The structure of S. antibioticus PNPase without bound RNA but with the phosphate analog tungstate bound at the PNPase catalytic sites was determined by X-ray crystallography and shows a trimeric multidomain protein with a central channel. The structural core has a novel duplicated architecture formed by association of two homologous domains. The tungstate derivative structure reveals the PNPase active site in the second of these core domains. Structure-based sequence analysis suggests that the pppGpp synthetase active site is located in the first core domain. CONCLUSIONS: This is the first structure of a PNPase and shows the structural basis for the trimer assembly, the arrangement of accessory RNA binding domains, and the likely catalytic residues of the PNPase active site. A possible function of the trimer channel is as a contribution to both the processivity of degradation and the regulation of PNPase action by RNA structural elements.
*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
 
== References ==
==About this Structure==
<references/>
1E3H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_antibioticus Streptomyces antibioticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E3H OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
A duplicated fold is the structural basis for polynucleotide phosphorylase catalytic activity, processivity, and regulation., Symmons MF, Jones GH, Luisi BF, Structure. 2000 Nov 15;8(11):1215-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11080643 11080643]
[[Category: Single protein]]
[[Category: Streptomyces antibioticus]]
[[Category: Streptomyces antibioticus]]
[[Category: Jones, G H.]]
[[Category: Jones GH]]
[[Category: Luisi, B F.]]
[[Category: Luisi BF]]
[[Category: Symmons, M F.]]
[[Category: Symmons MF]]
[[Category: atp:gtp diphosphotransferase]]
[[Category: polyribonucleotide transferase]]
[[Category: rna degradation]]
[[Category: rna processing]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:54:17 2008''
Retrieved from "https://proteopedia.org/1e3h"