1f2d: Difference between revisions

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-[[Image:1f2d.jpg|left|200px]]<br /><applet load="1f2d" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1f2d, resolution 2.0&Aring;" />
-'''1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE'''<br />
-==Overview==
+==1-AMINOCYCLOPROPANE-1-CARBOXYLATE DEAMINASE==
-The pyridoxal 5'-phosphate (PLP)-dependent enzyme, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) catalyzes a reaction, that involves a ring opening of cyclopropanoid amino acid, yielding, alpha-ketobutyrate and ammonia. Unlike other PLP-dependent enzymes, this, enzyme has no alpha-hydrogen atom in the substrate. Thus, a unique, mechanism for the bond cleavage is expected. The crystal structure of ACCD, from Hansenula saturnus has been determined at 2.0 A resolution by the, multiple wavelength anomalous diffraction method using mercury atoms as, anomalous scatterers. The model was built on the electron density map, which was obtained by the density averaging of multiple crystal forms. The, final model was refined to an R-factor of 22.5% and an R(free)-factor of, 26.8%. The ACCD folds into two domains, each of which has an open twisted, alpha/beta structure similar to the beta-subunit of tryptophan synthase., However, in ACCD, unlike in other members of the beta family of, PLP-dependent enzymes, PLP is buried deep in the molecule. The structure, provides the first view of the catalytic center of the cyclopropane ring, opening.
+<StructureSection load='1f2d' size='340' side='right'caption='[[1f2d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1f2d]] 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=1F2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F2D 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&#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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1f2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f2d OCA], [https://pdbe.org/1f2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f2d RCSB], [https://www.ebi.ac.uk/pdbsum/1f2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f2d 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/f2/1f2d_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=1f2d ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-F2D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Williopsis_saturnus Williopsis saturnus] with SO4 and PLP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/1-aminocyclopropane-1-carboxylate_deaminase 1-aminocyclopropane-1-carboxylate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.7 3.5.99.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F2D OCA].
+*[[Deaminase 3D structures|Deaminase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Crystal structure of 1-aminocyclopropane-1-carboxylate deaminase from Hansenula saturnus., Yao M, Ose T, Sugimoto H, Horiuchi A, Nakagawa A, Wakatsuki S, Yokoi D, Murakami T, Honma M, Tanaka I, J Biol Chem. 2000 Nov 3;275(44):34557-65. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10938279 10938279]
+[[Category: Cyberlindnera saturnus]]
-[[Category: 1-aminocyclopropane-1-carboxylate deaminase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Honma M]]
-[[Category: Williopsis saturnus]]
+[[Category: Horiuchi A]]
-[[Category: Honma, M.]]
+[[Category: Murakami T]]
-[[Category: Horiuchi, A.]]
+[[Category: Nakagawa A]]
-[[Category: Murakami, T.]]
+[[Category: Ose T]]
-[[Category: Nakagawa, A.]]
+[[Category: Sugimoto H]]
-[[Category: Ose, T.]]
+[[Category: Tanaka I]]
-[[Category: Sugimoto, H.]]
+[[Category: Wakatsuki S]]
-[[Category: Tanaka, I.]]
+[[Category: Yao M]]
-[[Category: Wakatsuki, S.]]
+[[Category: Yokoi D]]
-[[Category: Yao, M.]]
-[[Category: Yokoi, D.]]
-[[Category: PLP]]
-[[Category: SO4]]
-[[Category: 1-aminocyclopropane-1-carboxylate deaminase]]
-[[Category: carbon-carbon lyase]]
-[[Category: open twisted alpha/beta]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 14:32:43 2007''