3d2h: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:3d2h.png|left|200px]]
-{{STRUCTURE_3d2h|  PDB=3d2h  |  SCENE=  }}
+==Structure of berberine bridge enzyme from Eschscholzia californica, monoclinic crystal form==
+<StructureSection load='3d2h' size='340' side='right'caption='[[3d2h]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3d2h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Eschscholzia_californica Eschscholzia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2H 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]] 1.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FSH:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl+(2R,3S,4S)-5-[(4R)-6,7-dimethyl-2,3,5-trioxo-1H-spiro[imidazolidine-4,2-quinoxalin]-4(3H)-yl]-2,3,4-trihydroxypentyl+dihydrogen+diphosphate+(non-preferred+name)'>FSH</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=3d2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2h OCA], [https://pdbe.org/3d2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2h RCSB], [https://www.ebi.ac.uk/pdbsum/3d2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RETO_ESCCA RETO_ESCCA] Essential to the formation of benzophenanthridine alkaloids in the response of plants to pathogenic attack. Catalyzes the stereospecific conversion of the N-methyl moiety of (S)-reticuline into the berberine bridge carbon of (S)-scoulerine.
+== 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/d2/3d2h_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3d2h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Berberine bridge enzyme catalyzes the conversion of (S)-reticuline to (S)-scoulerine by formation of a carbon-carbon bond between the N-methyl group and the phenolic ring. We elucidated the structure of berberine bridge enzyme from Eschscholzia californica and determined the kinetic rates for three active site protein variants. Here we propose a catalytic mechanism combining base-catalyzed proton abstraction with concerted carbon-carbon coupling accompanied by hydride transfer from the N-methyl group to the N5 atom of the FAD cofactor.
-===Structure of berberine bridge enzyme from Eschscholzia californica, monoclinic crystal form===
+A concerted mechanism for berberine bridge enzyme.,Winkler A, Lyskowski A, Riedl S, Puhl M, Kutchan TM, Macheroux P, Gruber K Nat Chem Biol. 2008 Dec;4(12):739-41. Epub 2008 Oct 26. PMID:18953357<ref>PMID:18953357</ref>
-{{ABSTRACT_PUBMED_18953357}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3d2h" style="background-color:#fffaf0;"></div>
-[[3d2h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eschscholzia_californica Eschscholzia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2H OCA].
 ==See Also==
-*[[User:Andrzej Lyskowski|User:Andrzej Lyskowski]]
+*[[Reticuline oxidase|Reticuline oxidase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018953357</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Eschscholzia californica]]
-[[Category: Reticuline oxidase]]
+[[Category: Large Structures]]
-[[Category: Gruber, K.]]
+[[Category: Gruber K]]
-[[Category: Lyskowski, A.]]
+[[Category: Lyskowski A]]
-[[Category: Macheroux, P.]]
+[[Category: Macheroux P]]
-[[Category: Winkler, A.]]
+[[Category: Winkler A]]
-[[Category: Alakloid biosynthesis]]
-[[Category: Bi-covalent flavinylation]]
-[[Category: N-glycosylation]]
-[[Category: Oxidoreductase]]
-[[Category: P-cresol methylhydroxylase superfamily]]