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==STRUCTURE DETERMINATION OF THE TETRAHEDRAL AMINOPEPTIDASE TET2 FROM P. HORIKOSHII BY USE OF COMBINED SOLID-STATE NMR, SOLUTION-STATE NMR AND EM DATA 4.1 A, FOLLOWED BY REAL_SPACE_REFINEMENT AT 4.1 A==
==STRUCTURE DETERMINATION OF THE TETRAHEDRAL AMINOPEPTIDASE TET2 FROM P. HORIKOSHII BY USE OF COMBINED SOLID-STATE NMR, SOLUTION-STATE NMR AND EM DATA 4.1 A, FOLLOWED BY REAL_SPACE_REFINEMENT AT 4.1 A==
<SX load='6r8n' size='340' side='right' viewer='molstar' caption='[[6r8n]], [[Resolution|resolution]] 4.10&Aring;, [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
<SX load='6r8n' size='340' side='right' viewer='molstar' caption='[[6r8n]], [[Resolution|resolution]] 4.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6r8n]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6R8N FirstGlance]. <br>
<table><tr><td colspan='2'>[[6r8n]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R8N FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy , Hybrid , Solution NMR, [[Resolution|Resolution]] 4.1&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">frvX, PH1527 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6r8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8n OCA], [http://pdbe.org/6r8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r8n RCSB], [http://www.ebi.ac.uk/pdbsum/6r8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8n ProSAT]</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=6r8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r8n OCA], [https://pdbe.org/6r8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r8n RCSB], [https://www.ebi.ac.uk/pdbsum/6r8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r8n ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/TET_PYRHO TET_PYRHO]] Functions as an aminopeptidase, with a clear preference for leucine as the N-terminal amino acid. However, can also cleave moderately long polypeptide substrates of various compositions in a fairly unspecific manner. Has neither carboxypeptidase nor endoproteolytic activities, and it is devoid of N-terminal deblocking activity. Is involved in protein degradation, performing degradation of oligopeptides produced by the proteasome into single amino acids.<ref>PMID:15375159</ref> <ref>PMID:15713475</ref> <ref>PMID:15736957</ref>
[https://www.uniprot.org/uniprot/TET_PYRHO TET_PYRHO] Functions as an aminopeptidase, with a clear preference for leucine as the N-terminal amino acid. However, can also cleave moderately long polypeptide substrates of various compositions in a fairly unspecific manner. Has neither carboxypeptidase nor endoproteolytic activities, and it is devoid of N-terminal deblocking activity. Is involved in protein degradation, performing degradation of oligopeptides produced by the proteasome into single amino acids.<ref>PMID:15375159</ref> <ref>PMID:15713475</ref> <ref>PMID:15736957</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (&lt;30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 A by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 A resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.


Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex.,Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier JP, Guntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J Nat Commun. 2019 Jun 19;10(1):2697. doi: 10.1038/s41467-019-10490-9. PMID:31217444<ref>PMID:31217444</ref>
==See Also==
 
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6r8n" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</SX>
</SX>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii OT3]]
[[Category: Boisbouvier, J]]
[[Category: Boisbouvier J]]
[[Category: Colletier, J P]]
[[Category: Colletier J-P]]
[[Category: Effantin, G]]
[[Category: Effantin G]]
[[Category: Estrozi, L]]
[[Category: Estrozi L]]
[[Category: Favier, A]]
[[Category: Favier A]]
[[Category: Gauto, D]]
[[Category: Gauto D]]
[[Category: Schanda, P]]
[[Category: Schanda P]]
[[Category: Schoehn, G]]
[[Category: Schoehn G]]
[[Category: Aminopeptidase]]
[[Category: Oligomer]]
[[Category: Peptidase]]
[[Category: Peptide binding protein]]
[[Category: Protein quality control]]

Latest revision as of 16:03, 14 March 2024

STRUCTURE DETERMINATION OF THE TETRAHEDRAL AMINOPEPTIDASE TET2 FROM P. HORIKOSHII BY USE OF COMBINED SOLID-STATE NMR, SOLUTION-STATE NMR AND EM DATA 4.1 A, FOLLOWED BY REAL_SPACE_REFINEMENT AT 4.1 A

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