1j0c: Difference between revisions

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-[[Image:1j0c.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1j0c", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_1j0c|  PDB=1j0c  |  SCENE=  }}
-'''ACC deaminase mutated to catalytic residue'''
+==ACC deaminase mutated to catalytic residue==
+<StructureSection load='1j0c' size='340' side='right'caption='[[1j0c]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1j0c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cyberlindnera_saturnus Cyberlindnera saturnus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J0C FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.75&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1j0c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j0c OCA], [https://pdbe.org/1j0c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j0c RCSB], [https://www.ebi.ac.uk/pdbsum/1j0c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j0c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/1A1D_CYBSA 1A1D_CYBSA] Catalyzes a cyclopropane ring-opening reaction, the irreversible conversion of 1-aminocyclopropane-1-carboxylate (ACC) to ammonia and alpha-ketobutyrate.
+== 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/j0/1j0c_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=1j0c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The pyridoxal 5'-phosphate-dependent enzymes have been evolved to catalyze diverse substrates and to cause the reaction to vary. 1-Aminocyclopropane-1-carboxylate deaminase catalyzes the cyclopropane ring-opening reaction followed by deamination specifically. Since it was discovered in 1978, the enzyme has been widely investigated from the mechanistic and physiological viewpoints because the substrate is a precursor of the plant hormone ethylene and the enzymatic reaction includes a cyclopropane ring-opening. We have previously reported the crystal structure of the native enzyme. Here we report the crystal structures of the two reaction intermediates created by the mutagenesis complexed with the substrate. The substrate was validated in the active site of two forms: 1). covalent-bonded external aldimine with the coenzyme in the K51T form and 2). the non-covalent interaction around the coenzyme in the Y295F form. The orientations of the substrate in both structures were quite different form each other. In concert with other site-specific mutation experiments, this experiment revealed the ingenious and unique strategies that are used to achieve the specific activity. The substrate incorporated into the active site is reactivated by a two-phenol charge relay system to lead to the formation of a Schiff base with the coenzyme. The catalytic Lys51 residue may play a novel role to abstract the methylene proton from the substrate in cooperation with other factors, the carboxylate group of the substrate and the electron-adjusting apparatuses of the coenzyme.
-==Overview==
+Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction.,Ose T, Fujino A, Yao M, Watanabe N, Honma M, Tanaka I J Biol Chem. 2003 Oct 17;278(42):41069-76. Epub 2003 Jul 26. PMID:12882962<ref>PMID:12882962</ref>
-The pyridoxal 5'-phosphate-dependent enzymes have been evolved to catalyze diverse substrates and to cause the reaction to vary. 1-Aminocyclopropane-1-carboxylate deaminase catalyzes the cyclopropane ring-opening reaction followed by deamination specifically. Since it was discovered in 1978, the enzyme has been widely investigated from the mechanistic and physiological viewpoints because the substrate is a precursor of the plant hormone ethylene and the enzymatic reaction includes a cyclopropane ring-opening. We have previously reported the crystal structure of the native enzyme. Here we report the crystal structures of the two reaction intermediates created by the mutagenesis complexed with the substrate. The substrate was validated in the active site of two forms: 1). covalent-bonded external aldimine with the coenzyme in the K51T form and 2). the non-covalent interaction around the coenzyme in the Y295F form. The orientations of the substrate in both structures were quite different form each other. In concert with other site-specific mutation experiments, this experiment revealed the ingenious and unique strategies that are used to achieve the specific activity. The substrate incorporated into the active site is reactivated by a two-phenol charge relay system to lead to the formation of a Schiff base with the coenzyme. The catalytic Lys51 residue may play a novel role to abstract the methylene proton from the substrate in cooperation with other factors, the carboxylate group of the substrate and the electron-adjusting apparatuses of the coenzyme.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-J0C is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Williopsis_saturnus Williopsis saturnus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J0C OCA].
+</div>
+<div class="pdbe-citations 1j0c" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Reaction intermediate structures of 1-aminocyclopropane-1-carboxylate deaminase: insight into PLP-dependent cyclopropane ring-opening reaction., Ose T, Fujino A, Yao M, Watanabe N, Honma M, Tanaka I, J Biol Chem. 2003 Oct 17;278(42):41069-76. Epub 2003 Jul 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12882962 12882962]
+*[[Deaminase 3D structures|Deaminase 3D structures]]
-[[Category: 1-aminocyclopropane-1-carboxylate deaminase]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Williopsis saturnus]]
+__TOC__
-[[Category: Fujino, A.]]
+</StructureSection>
-[[Category: Honma, M.]]
+[[Category: Cyberlindnera saturnus]]
-[[Category: Ose, T.]]
+[[Category: Large Structures]]
-[[Category: Tanaka, I.]]
+[[Category: Fujino A]]
-[[Category: Yao, M.]]
+[[Category: Honma M]]
-[[Category: Plp dependent b group]]
+[[Category: Ose T]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:38:50 2008''
+[[Category: Tanaka I]]
+[[Category: Yao M]]