1c21: Difference between revisions

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-[[Image:1c21.gif|left|200px]]
-<!--
+==E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1c21", creates the "Structure Box" on the page.
+<StructureSection load='1c21' size='340' side='right'caption='[[1c21]], [[Resolution|resolution]] 1.80&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'>[[1c21]] 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=1C21 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C21 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]] 1.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-{{STRUCTURE_1c21|  PDB=1c21  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c21 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c21 OCA], [https://pdbe.org/1c21 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c21 RCSB], [https://www.ebi.ac.uk/pdbsum/1c21 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c21 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/c2/1c21_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=1c21 ConSurf].
+<div style="clear:both"></div>
-'''E. COLI METHIONINE AMINOPEPTIDASE: METHIONINE COMPLEX'''
+==See Also==
+*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
+== References ==
-==Overview==
+<references/>
-In an effort to differentiate between alternative mechanistic schemes that have been postulated for Escherichia coli methionine aminopeptidase (eMetAP), the modes of binding of a series of products and phosphorus-based transition-state analogues were determined by X-ray crystallography. Methionine phosphonate, norleucine phosphonate, and methionine phosphinate bind with the N-terminal group interacting with Co2 and with the respective phosphorus oxygens binding between the metals, interacting in a bifurcated manner with Co1 and His178 and hydrogen bonded to His79. In contrast, the reaction product methionine and its analogue trifluoromethionine lose interactions with Co1 and His79. The interactions with the transition-state analogues are, in general, very similar to those seen previously for the complex of the enzyme with a bestatin-based inhibitor. The mode of interaction of His79 is, however, different. In the case of the bestatin-based inhibitor, His79 interacts with atoms in the peptide bond between the P(1)' and P(2)' residues. In the present transition-state analogues, however, the histidine moves 1.2 A toward the metal center and hydrogen bonds with the atom that corresponds to the nitrogen of the scissile peptide bond (i.e., between the P(1) and P(1)' residues). These observations tend to support one of the mechanistic schemes for eMetAP considered before, although with a revision in the role played by His79. The results also suggest parallels between the mechanism of action of methionine aminopeptidase and other "pita-bread" enzymes including aminopeptidase P and creatinase.
+__TOC__
+</StructureSection>
-==About this Structure==
-C21 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=1C21 OCA].
-==Reference==
-Insights into the mechanism of Escherichia coli methionine aminopeptidase from the structural analysis of reaction products and phosphorus-based transition-state analogues., Lowther WT, Zhang Y, Sampson PB, Honek JF, Matthews BW, Biochemistry. 1999 Nov 9;38(45):14810-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10555963 10555963]
 [[Category: Escherichia coli]]
-[[Category: Methionyl aminopeptidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Honek JF]]
-[[Category: Honek, J F.]]
+[[Category: Lowther WT]]
-[[Category: Lowther, W T.]]
+[[Category: Matthews BW]]
-[[Category: Matthews, B W.]]
+[[Category: Sampson PB]]
-[[Category: Sampson, P B.]]
+[[Category: Zhang Y]]
-[[Category: Zhang, Y.]]
-[[Category: Hydrolase]]
-[[Category: Product complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 12:14:21 2008''