2bii: Difference between revisions

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-{{Seed}}
-[[Image:2bii.png|left|200px]]
-<!--
+==crystal structure of nitrate-reducing fragment of assimilatory nitrate reductase from Pichia angusta==
-The line below this paragraph, containing "STRUCTURE_2bii", creates the "Structure Box" on the page.
+<StructureSection load='2bii' size='340' side='right'caption='[[2bii]], [[Resolution|resolution]] 1.70&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'>[[2bii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ogataea_angusta Ogataea angusta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BII 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MTV:(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)'>MTV</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2bii|  PDB=2bii  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bii OCA], [https://pdbe.org/2bii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bii RCSB], [https://www.ebi.ac.uk/pdbsum/2bii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bii ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NIA_PICAN NIA_PICAN] Nitrate reductase is a key enzyme involved in the first step of nitrate assimilation in plants, fungi and bacteria.
+== 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/bi/2bii_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=2bii ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nitrate assimilation in autotrophs provides most of the reduced nitrogen on earth. In eukaryotes, reduction of nitrate to nitrite is catalyzed by the molybdenum-containing NAD(P)H:nitrate reductase (NR; EC 1.7.1.1-3). In addition to the molybdenum center, NR contains iron-heme and flavin adenine dinucleotide as redox cofactors involved in an internal electron transport chain from NAD(P)H to nitrate. Recombinant, catalytically active Pichia angusta nitrate-reducing, molybdenum-containing fragment (NR-Mo) was expressed in P. pastoris and purified. Crystal structures for NR-Mo were determined at 1.7 and 2.6 angstroms. These structures revealed a unique slot for binding nitrate in the active site and identified key Arg and Trp residues potentially involved in nitrate binding. Dimeric NR-Mo is similar in overall structure to sulfite oxidases, with significant differences in the active site. Sulfate bound in the active site caused conformational changes, as compared with the unbound enzyme. Four ordered water molecules located in close proximity to Mo define a nitrate binding site, a penta-coordinated reaction intermediate, and product release. Because yeast NAD(P)H:NR is representative of the family of eukaryotic NR, we propose a general mechanism for nitrate reduction catalysis.
-===CRYSTAL STRUCTURE OF NITRATE-REDUCING FRAGMENT OF ASSIMILATORY NITRATE REDUCTASE FROM PICHIA ANGUSTA===
+Structural basis of eukaryotic nitrate reduction: crystal structures of the nitrate reductase active site.,Fischer K, Barbier GG, Hecht HJ, Mendel RR, Campbell WH, Schwarz G Plant Cell. 2005 Apr;17(4):1167-79. Epub 2005 Mar 16. PMID:15772287<ref>PMID:15772287</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bii" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15772287}}, adds the Publication Abstract to the page
+*[[Nitrate reductase|Nitrate reductase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15772287 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15772287}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BII is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pichia_angusta Pichia angusta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BII OCA].
+[[Category: Ogataea angusta]]
+[[Category: Barbier G]]
-==Reference==
+[[Category: Campbell WH]]
-Structural basis of eukaryotic nitrate reduction: crystal structures of the nitrate reductase active site., Fischer K, Barbier GG, Hecht HJ, Mendel RR, Campbell WH, Schwarz G, Plant Cell. 2005 Apr;17(4):1167-79. Epub 2005 Mar 16. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15772287 15772287]
+[[Category: Fischer K]]
-[[Category: Pichia angusta]]
+[[Category: Hecht H-J]]
-[[Category: Single protein]]
+[[Category: Mendel RR]]
-[[Category: Barbier, G.]]
+[[Category: Schwarz G]]
-[[Category: Campbell, W H.]]
-[[Category: Fischer, K.]]
-[[Category: Hecht, H J.]]
-[[Category: Mendel, R R.]]
-[[Category: Schwarz, G.]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Heme]]
-[[Category: Molybdenum]]
-[[Category: Nadp]]
-[[Category: Nitrate assimilation]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 06:14:39 2008''