2p99: Difference between revisions

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-[[Image:2p99.jpg|left|200px]]
- {{Structure
+==E. coli methionine aminopeptidase monometalated with inhibitor YE6==
-|PDB= 2p99 |SIZE=350|CAPTION= <scene name='initialview01'>2p99</scene>, resolution 1.800&Aring;
+<StructureSection load='2p99' size='340' side='right'caption='[[2p99]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> and <scene name='pdbligand=YE6:[5-(2-CHLOROPHENYL)-2-FUROYL]DIAZENE'>YE6</scene>
+<table><tr><td colspan='2'>[[2p99]] is a 1 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=2P99 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P99 FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Methionyl_aminopeptidase Methionyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.18 3.4.11.18]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-|GENE= map ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=YE6:5-(2-CHLOROPHENYL)FURAN-2-CARBOHYDRAZIDE'>YE6</scene></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=2p99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p99 OCA], [https://pdbe.org/2p99 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p99 RCSB], [https://www.ebi.ac.uk/pdbsum/2p99 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p99 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MAP1_ECOLI MAP1_ECOLI] Removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Requires deformylation of the N(alpha)-formylated initiator methionine before it can be hydrolyzed.[HAMAP-Rule:MF_01974]<ref>PMID:20521764</ref> <ref>PMID:3027045</ref>
+== 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/p9/2p99_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=2p99 ConSurf].
+<div style="clear:both"></div>
-'''E. coli methionine aminopeptidase monometalated with inhibitor YE6'''
+==See Also==
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
+== References ==
-==Overview==
+<references/>
-Two divalent metal ions are commonly seen in the active-site cavity of methionine aminopeptidase, and at least one of the metal ions is directly involved in catalysis. Although ample structural and functional information is available for dimetalated enzyme, methionine aminopeptidase likely functions as a monometalated enzyme under physiological conditions. Information on structure, as well as catalysis and inhibition, of the monometalated enzyme is lacking. By improving conditions of high-throughput screening, we identified a unique inhibitor with specificity toward the monometalated enzyme. Kinetic characterization indicates a mutual exclusivity in binding between the inhibitor and the second metal ion at the active site. This is confirmed by X-ray structure, and this inhibitor coordinates with the first metal ion and occupies the space normally occupied by the second metal ion. Kinetic and structural analyses of the inhibition by this and other inhibitors provide insight in designing effective inhibitors of methionine aminopeptidase.
+__TOC__
+</StructureSection>
-==About this Structure==
-P99 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=2P99 OCA].
-==Reference==
-Inhibition of monometalated methionine aminopeptidase: inhibitor discovery and crystallographic analysis., Huang M, Xie SX, Ma ZQ, Huang QQ, Nan FJ, Ye QZ, J Med Chem. 2007 Nov 15;50(23):5735-42. Epub 2007 Oct 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17948983 17948983]
 [[Category: Escherichia coli]]
-[[Category: Methionyl aminopeptidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Ye Q]]
-[[Category: Ye, Q.]]
-[[Category: MN]]
-[[Category: NA]]
-[[Category: YE6]]
-[[Category: enzyme-inhibitor complex]]
-[[Category: hydrolase]]
-[[Category: metalloenzyme]]
-[[Category: mn(ii)-form]]
-[[Category: monometalated]]
-[[Category: mononuclear]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:10:24 2008''