2h5u: 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: @@
-{{Seed}}
-[[Image:2h5u.png|left|200px]]
-<!--
+==Crystal structure of laccase from Cerrena maxima at 1.9A resolution==
-The line below this paragraph, containing "STRUCTURE_2h5u", creates the "Structure Box" on the page.
+<StructureSection load='2h5u' size='340' side='right'caption='[[2h5u]], [[Resolution|resolution]] 1.90&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'>[[2h5u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Trametes_maxima Trametes maxima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H5U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H5U FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NIY:META-NITRO-TYROSINE'>NIY</scene></td></tr>
-{{STRUCTURE_2h5u|  PDB=2h5u  |  SCENE=  }}
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kya|1kya]]</div></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Laccase Laccase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.2 1.10.3.2] </span></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=2h5u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h5u OCA], [https://pdbe.org/2h5u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h5u RCSB], [https://www.ebi.ac.uk/pdbsum/2h5u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h5u ProSAT]</span></td></tr>
+</table>
+== 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/h5/2h5u_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=2h5u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 A resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccase structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 A (R factor = 18.953%; R(free) = 23.835; r.m.s.d. bond lengths, 0.06 A; r.m.s.d. bond angles, 1.07 degrees) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 A X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO(2) substituents.
-===Crystal structure of laccase from Cerrena maxima at 1.9A resolution===
+Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima.,Lyashenko AV, Zhukhlistova NE, Gabdoulkhakov AG, Zhukova YN, Voelter W, Zaitsev VN, Bento I, Stepanova EV, Kachalova GS, Koroleva OV, Cherkashyn EA, Tishkov VI, Lamzin VS, Schirwitz K, Morgunova EY, Betzel C, Lindley PF, Mikhailov AM Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Oct 1;62(Pt, 10):954-7. Epub 2006 Sep 19. PMID:17012782<ref>PMID:17012782</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2h5u" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17012782}}, adds the Publication Abstract to the page
+*[[Laccase 3D structures|Laccase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17012782 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17012782}}
+__TOC__
+</StructureSection>
-==About this Structure==
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H5U OCA].
-==Reference==
-Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima., Lyashenko AV, Zhukhlistova NE, Gabdoulkhakov AG, Zhukova YN, Voelter W, Zaitsev VN, Bento I, Stepanova EV, Kachalova GS, Koroleva OV, Cherkashyn EA, Tishkov VI, Lamzin VS, Schirwitz K, Morgunova EY, Betzel C, Lindley PF, Mikhailov AM, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Oct 1;62(Pt, 10):954-7. Epub 2006 Sep 19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17012782 17012782]
 [[Category: Laccase]]
-[[Category: Bento, I.]]
+[[Category: Large Structures]]
-[[Category: Betzel, C.]]
+[[Category: Trametes maxima]]
-[[Category: Gabdoulkhakov, A G.]]
+[[Category: Bento, I]]
-[[Category: Lamzin, V S.]]
+[[Category: Betzel, C]]
-[[Category: Lindley, P F.]]
+[[Category: Gabdoulkhakov, A G]]
-[[Category: Lyashenko, A V.]]
+[[Category: Lamzin, V S]]
-[[Category: Mikhailov, A M.]]
+[[Category: Lindley, P F]]
-[[Category: Zaitsev, V N.]]
+[[Category: Lyashenko, A V]]
-[[Category: Zhukhlistova, N E.]]
+[[Category: Mikhailov, A M]]
-[[Category: Zhukova, Y N.]]
+[[Category: Zaitsev, V N]]
+[[Category: Zhukhlistova, N E]]
+[[Category: Zhukova, Y N]]
 [[Category: Blue multi-copper enzyme]]
 [[Category: Crystal]]
 [[Category: Laccase from cerrena maxima]]
+[[Category: Oxidoreductase]]
 [[Category: Purification]]
 [[Category: X-ray analyse]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 00:01:56 2008''