2z3m: Difference between revisions

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{{Seed}}
[[Image:2z3m.png|left|200px]]


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==complex structure of LF-transferase and dAF==
The line below this paragraph, containing "STRUCTURE_2z3m", creates the "Structure Box" on the page.
<StructureSection load='2z3m' size='340' side='right'caption='[[2z3m]], [[Resolution|resolution]] 2.70&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'>[[2z3m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z3M 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]] 2.7&#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=3D1:(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL'>3D1</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
{{STRUCTURE_2z3m|  PDB=2z3m  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z3m OCA], [https://pdbe.org/2z3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z3m RCSB], [https://www.ebi.ac.uk/pdbsum/2z3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z3m ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LFTR_ECOLI LFTR_ECOLI] Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine.
== 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/z3/2z3m_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2z3m ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.


===complex structure of LF-transferase and dAF===
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.,Watanabe K, Toh Y, Suto K, Shimizu Y, Oka N, Wada T, Tomita K Nature. 2007 Oct 18;449(7164):867-71. Epub 2007 Sep 23. PMID:17891155<ref>PMID:17891155</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_17891155}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2z3m" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 17891155 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17891155}}
__TOC__
 
</StructureSection>
==About this Structure==
2Z3M is a 2 chains structure of sequences 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=2Z3M OCA].
 
==Reference==
<ref group="xtra">PMID:17891155</ref><references group="xtra"/>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Leucyltransferase]]
[[Category: Large Structures]]
[[Category: Toh, Y.]]
[[Category: Toh Y]]
[[Category: Tomita, K.]]
[[Category: Tomita K]]
[[Category: Watanabe, K.]]
[[Category: Watanabe K]]
[[Category: Lf-transferase]]
 
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Retrieved from "https://proteopedia.org/2z3m"