2p6f: Difference between revisions

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<StructureSection load='2p6f' size='340' side='right'caption='[[2p6f]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
<StructureSection load='2p6f' size='340' side='right'caption='[[2p6f]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2p6f]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P6F FirstGlance]. <br>
<table><tr><td colspan='2'>[[2p6f]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P6F FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GN8:(Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE'>GN8</scene>, <scene name='pdbligand=MYA:TETRADECANOYL-COA'>MYA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2p6e|2p6e]], [[2p6g|2p6g]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GN8:(Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE'>GN8</scene>, <scene name='pdbligand=MYA:TETRADECANOYL-COA'>MYA</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">850892 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glycylpeptide_N-tetradecanoyltransferase Glycylpeptide N-tetradecanoyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.97 2.3.1.97] </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=2p6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p6f OCA], [https://pdbe.org/2p6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p6f RCSB], [https://www.ebi.ac.uk/pdbsum/2p6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p6f 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=2p6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p6f OCA], [https://pdbe.org/2p6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p6f RCSB], [https://www.ebi.ac.uk/pdbsum/2p6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p6f ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/NMT_YEAST NMT_YEAST]] Adds a myristoyl group to the N-terminal glycine residue of certain cellular proteins. Substrate specificity requires an N-terminal glycine in the nascent polypeptide substrates. Uncharged amino acids are preferred at position 2 while neutral residues are favored at positions 3 and 4. Ser is present at position 5 in almost all known N-myristoyl proteins and Lys is commonly encountered at postion 6.  
[https://www.uniprot.org/uniprot/NMT_YEAST NMT_YEAST] Adds a myristoyl group to the N-terminal glycine residue of certain cellular proteins. Substrate specificity requires an N-terminal glycine in the nascent polypeptide substrates. Uncharged amino acids are preferred at position 2 while neutral residues are favored at positions 3 and 4. Ser is present at position 5 in almost all known N-myristoyl proteins and Lys is commonly encountered at postion 6.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=2p6f ConSurf].
</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=2p6f ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Protein N-myristoylation catalyzed by myristoyl-CoA:protein N-myristoyltransferase (NMT) plays an important role in a variety of critical cellular processes and thus is an attractive target for development of antifungal drugs. We report here three crystal structures of Saccharomyces cerevisiae NMT: in binary complex with myristoyl-CoA (MYA) alone and in two ternary complexes involving MYA and two different non-peptidic inhibitors. In all three structures, the majority of the N-terminal region, absent in all previously reported structures, forms a well defined motif that is located in the vicinity of the peptide substrate-binding site and is involved in the binding of MYA. The Ab loop, which might be involved in substrate recognition, adopts an open conformation, whereas a loop of the N-terminal region (residues 22-24) that covers the top of the substrate-binding site is in the position occupied by the Ab loop when in the closed conformation. Structural comparisons with other NMTs, together with mutagenesis data, suggest that the N-terminal region of NMT plays an important role in the binding of both MYA and peptide substrate, but not in subsequent steps of the catalytic mechanism. The two inhibitors occupy the peptide substrate-binding site and interact with the protein through primarily hydrophobic contacts. Analyses of the inhibitorenzyme interactions provide valuable information for further improvement of antifungal inhibitors targeting NMT.
Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors reveal the functional roles of the N-terminal region.,Wu J, Tao Y, Zhang M, Howard MH, Gutteridge S, Ding J J Biol Chem. 2007 Jul 27;282(30):22185-94. Epub 2007 May 18. PMID:17513302<ref>PMID:17513302</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2p6f" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 18824]]
[[Category: Glycylpeptide N-tetradecanoyltransferase]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ding, J]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Wu, J]]
[[Category: Ding J]]
[[Category: Antifungal drug]]
[[Category: Wu J]]
[[Category: Non-peptidic inhibitor]]
[[Category: Transferase]]
Retrieved from "https://proteopedia.org/2p6f"