2bwi: Difference between revisions

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-[[Image:2bwi.gif|left|200px]]
- {{Structure
+==Atomic Resolution Structure of Nitrite -soaked Achromobacter cycloclastes Cu Nitrite Reductase==
-|PDB= 2bwi |SIZE=350|CAPTION= <scene name='initialview01'>2bwi</scene>, resolution 1.10&Aring;
+<StructureSection load='2bwi' size='340' side='right'caption='[[2bwi]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Act+Binding+Site+For+Chain+A'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>
+<table><tr><td colspan='2'>[[2bwi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BWI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BWI FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.1&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bwi OCA], [https://pdbe.org/2bwi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bwi RCSB], [https://www.ebi.ac.uk/pdbsum/2bwi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bwi ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bwi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bwi OCA], [http://www.ebi.ac.uk/pdbsum/2bwi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2bwi RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY]
+== 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/bw/2bwi_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=2bwi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.
-'''ATOMIC RESOLUTION STRUCTURE OF NITRITE-SOAKED ACHROMOBACTER CYCLOCLASTES CU NITRITE REDUCTASE'''
+Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism.,Antonyuk SV, Strange RW, Sawers G, Eady RR, Hasnain SS Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12041-6. Epub 2005 Aug 10. PMID:16093314<ref>PMID:16093314</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2bwi" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using "crystal harvesting" and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 A, two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 A and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 A resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct.
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-BWI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BWI OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism., Antonyuk SV, Strange RW, Sawers G, Eady RR, Hasnain SS, Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12041-6. Epub 2005 Aug 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16093314 16093314]
 [[Category: Achromobacter cycloclastes]]
-[[Category: Nitrite reductase (NO-forming)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Antonyuk SV]]
-[[Category: Antonyuk, S V.]]
+[[Category: Eady RR]]
-[[Category: Eady, R R.]]
+[[Category: Hasnain SS]]
-[[Category: Hasnain, S S.]]
+[[Category: Sawers G]]
-[[Category: Sawers, G.]]
+[[Category: Strange RW]]
-[[Category: Strange, R W.]]
-[[Category: denitrification,catalysis,enzyme mechanism,oxidoreductase]]
-[[Category: nitrate assimilation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:12:49 2008''