3ml1: Difference between revisions

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-[[Image:3ml1.jpg|left|200px]]
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+==Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator==
-The line below this paragraph, containing "STRUCTURE_3ml1", creates the "Structure Box" on the page.
+<StructureSection load='3ml1' size='340' side='right'caption='[[3ml1]], [[Resolution|resolution]] 1.60&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'>[[3ml1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cupriavidus_necator_H16 Cupriavidus necator H16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ML1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ML1 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MOS:DIOXOTHIOMOLYBDENUM(VI)+ION'>MOS</scene></td></tr>
-{{STRUCTURE_3ml1|  PDB=3ml1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ml1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ml1 OCA], [https://pdbe.org/3ml1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ml1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ml1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ml1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAPB_CUPNH NAPB_CUPNH] Electron transfer subunit of the periplasmic nitrate reductase complex NapAB. Receives electrons from the membrane-anchored tetraheme c-type NapC protein and transfers these to NapA subunit, thus allowing electron flow between membrane and periplasm. Essential for periplasmic nitrate reduction with nitrate as the terminal electron acceptor.<ref>PMID:8376334</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The periplasmic nitrate reductase (NapAB) from Cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein comprises a large catalytic subunit (NapA, 91 kDa) containing the molybdenum active site plus one [4Fe-4S] cluster, as well as a small subunit (NapB, 17 kDa), which is a diheme c-type cytochrome involved in electron transfer. Crystals of the oxidized form of the enzyme diffracted beyond 1.5 A at the European Synchrotron Radiation Facility. This is the highest resolution reported to date for a nitrate reductase, providing true atomic details of the protein active center, and this showed further evidence on the molybdenum coordination sphere, corroborating previous data on the related Desulfovibrio desulfuricans NapA. The molybdenum atom is bound to a total of six sulfur atoms, with no oxygen ligands or water molecules in the vicinity. In the present work, we were also able to prepare partially reduced crystals that revealed two alternate conformations of the Mo-coordinating cysteine. This crystal form was obtained by soaking dithionite into crystals grown in the presence of the ionic liquid [C(4)mim]Cl(-). In addition, UV-Vis and EPR spectroscopy studies showed that the periplasmic nitrate reductase from C. necator might work at unexpectedly high redox potentials when compared to all periplasmic nitrate reductases studied to date.
-===Crystal Structure of the Periplasmic Nitrate Reductase from Cupriavidus necator===
+The Crystal Structure of Cupriavidus necator Nitrate Reductase in Oxidized and Partially Reduced States.,Coelho C, Gonzalez PJ, Moura JJ, Moura I, Trincao J, Joao Romao M J Mol Biol. 2011 Mar 23. PMID:21419779<ref>PMID:21419779</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ml1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21419779}}, adds the Publication Abstract to the page
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21419779 is the PubMed ID number.
+*[[Nitrate reductase|Nitrate reductase]]
--->
+== References ==
-{{ABSTRACT_PUBMED_21419779}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[3ml1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cupriavidus_necator Cupriavidus necator]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ML1 OCA].
+[[Category: Cupriavidus necator H16]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Coelho C]]
-<ref group="xtra">PMID:21419779</ref><references group="xtra"/>
+[[Category: Romao MJ]]
-[[Category: Cupriavidus necator]]
+[[Category: Trincao J]]
-[[Category: Nitrate reductase]]
-[[Category: Coelho, C.]]
-[[Category: Romao, M J.]]
-[[Category: Trincao, J.]]