3n3b: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image: | ==Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide== | ||
<StructureSection load='3n3b' size='340' side='right' caption='[[3n3b]], [[Resolution|resolution]] 2.36Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3n3b]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N3B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N3B FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n37|3n37]], [[3n38|3n38]], [[3n39|3n39]], [[3n3a|3n3a]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b2676, JW2651, nrdF, ygaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), nrdI, ygaO, b2674, JW2649 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonucleoside-diphosphate_reductase Ribonucleoside-diphosphate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.4.1 1.17.4.1] </span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3n3b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n3b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n3b RCSB], [http://www.ebi.ac.uk/pdbsum/3n3b PDBsum]</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/n3/3n3b_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/chain_selection.php?pdb_ID=2ata ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)(2)-tyrosyl radical (Y*) or a Fe(III)(2)-Y* cofactor in the NrdF subunit. Whereas Fe(III)(2)-Y* can self-assemble from Fe(II)(2)-NrdF and O(2), activation of Mn(II)(2)-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O(2). The crystal structures reported here of E. coli Mn(II)(2)-NrdF and Fe(II)(2)-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)(2)-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)(2) active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)(2)-Y* cofactor assembly. | |||
Structural Basis for Activation of Class Ib Ribonucleotide Reductase.,Boal AK, Cotruvo JA Jr, Stubbe J, Rosenzweig AC Science. 2010 Aug 5. PMID:20688982<ref>PMID:20688982</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
==See Also== | ==See Also== | ||
*[[Ribonucleotide reductase|Ribonucleotide reductase]] | *[[Ribonucleotide reductase|Ribonucleotide reductase]] | ||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Ribonucleoside-diphosphate reductase]] | [[Category: Ribonucleoside-diphosphate reductase]] | ||
[[Category: Boal, A K | [[Category: Boal, A K]] | ||
[[Category: Cotruvo, J A | [[Category: Cotruvo, J A]] | ||
[[Category: Rosenzweig, A C | [[Category: Rosenzweig, A C]] | ||
[[Category: Stubbe, J | [[Category: Stubbe, J]] | ||
[[Category: Dimanganese cluster]] | [[Category: Dimanganese cluster]] | ||
[[Category: Flavoprotein]] | [[Category: Flavoprotein]] | ||
Revision as of 12:24, 9 December 2014
Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped PeroxideRibonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI with a Trapped Peroxide
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe class Ib ribonucleotide reductase of Escherichia coli can initiate reduction of nucleotides to deoxynucleotides with either a Mn(III)(2)-tyrosyl radical (Y*) or a Fe(III)(2)-Y* cofactor in the NrdF subunit. Whereas Fe(III)(2)-Y* can self-assemble from Fe(II)(2)-NrdF and O(2), activation of Mn(II)(2)-NrdF requires a reduced flavoprotein, NrdI, proposed to form the oxidant for cofactor assembly by reduction of O(2). The crystal structures reported here of E. coli Mn(II)(2)-NrdF and Fe(II)(2)-NrdF reveal different coordination environments, suggesting distinct initial binding sites for the oxidants during cofactor activation. In the structures of Mn(II)(2)-NrdF in complex with reduced and oxidized NrdI, a continuous channel connects the NrdI flavin cofactor to the NrdF Mn(II)(2) active site. Crystallographic detection of a putative peroxide in this channel supports the proposed mechanism of Mn(III)(2)-Y* cofactor assembly. Structural Basis for Activation of Class Ib Ribonucleotide Reductase.,Boal AK, Cotruvo JA Jr, Stubbe J, Rosenzweig AC Science. 2010 Aug 5. PMID:20688982[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||