This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2p6e

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2p6e" size="450" color="white" frame="true" align="right" spinBox="true" caption="2p6e, resolution 2.900&Aring;" /> '''Crystal structures ...)
Current revision (13:53, 13 March 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2p6e.jpg|left|200px]]<br /><applet load="2p6e" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2p6e, resolution 2.900&Aring;" />
 
-
'''Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA'''<br />
 
-
==Overview==
+
==Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA==
-
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; as a binary complex with myristoyl-CoA, alone and two ternary complexes involving myristoyl-CoA 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 myristoyl-CoA., The Ab loop, which might be involved in substrate recognition, adopts an, open conformation; while 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 myristoyl-CoA and peptide substrate, but not in subsequent steps of, the catalytic mechanism. The two inhibitors are found occupying the, peptide substrate binding site and interact with the protein through, primarily hydrophobic contacts. Analyses of the inhibitor-enzyme, interactions provide valuable information for further improvement of, antifungal inhibitors targeting NMT.
+
<StructureSection load='2p6e' size='340' side='right'caption='[[2p6e]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2p6e]] 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=2P6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P6E FirstGlance]. <br>
-
2P6E is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MYA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycylpeptide_N-tetradecanoyltransferase Glycylpeptide N-tetradecanoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.97 2.3.1.97] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2P6E OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MYA:TETRADECANOYL-COA'>MYA</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2p6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p6e OCA], [https://pdbe.org/2p6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p6e RCSB], [https://www.ebi.ac.uk/pdbsum/2p6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p6e ProSAT]</span></td></tr>
-
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 M, Gutteridge S, Ding J, J Biol Chem. 2007 May 18;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17513302 17513302]
+
</table>
-
[[Category: Glycylpeptide N-tetradecanoyltransferase]]
+
== 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.
 +
== 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/p6/2p6e_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=2p6e ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Ding J]]
-
[[Category: Ding, J.]]
+
[[Category: Wu J]]
-
[[Category: Wu, J.]]
+
-
[[Category: MYA]]
+
-
[[Category: n-myristoyltransferase]]
+
-
[[Category: substrate recognition]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:26:01 2007''
+

Current revision

Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA

PDB ID 2p6e

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2p6e"
Personal tools