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2z3k

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{{Seed}}
 
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[[Image:2z3k.png|left|200px]]
 
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==complex structure of LF-transferase and rAF==
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The line below this paragraph, containing "STRUCTURE_2z3k", creates the "Structure Box" on the page.
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<StructureSection load='2z3k' size='340' side='right'caption='[[2z3k]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2z3k]] 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=2Z3K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z3K FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#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=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=XYA:2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL'>XYA</scene></td></tr>
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{{STRUCTURE_2z3k| PDB=2z3k | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z3k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z3k OCA], [https://pdbe.org/2z3k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z3k RCSB], [https://www.ebi.ac.uk/pdbsum/2z3k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z3k ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z3/2z3k_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2z3k ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===complex structure of LF-transferase and rAF===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_17891155}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2z3k" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 17891155 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17891155}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2Z3K is a [[Single protein]] structure of sequence 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=2Z3K OCA].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17891155 17891155]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Leucyltransferase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Toh Y]]
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[[Category: Toh, Y.]]
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[[Category: Tomita K]]
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[[Category: Tomita, K.]]
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[[Category: Watanabe K]]
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[[Category: Watanabe, K.]]
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[[Category: Lf-transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 18:01:55 2008''
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Current revision

complex structure of LF-transferase and rAF

PDB ID 2z3k

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