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3ir6

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[[Image:3ir6.png|left|200px]]
 
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{{STRUCTURE_3ir6| PDB=3ir6 | SCENE= }}
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==Crystal structure of NarGHI mutant NarG-H49S==
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<StructureSection load='3ir6' size='340' side='right'caption='[[3ir6]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3ir6]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IR6 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGA:(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL+OCTANOATE'>AGA</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1q16|1q16]], [[3ir5|3ir5]], [[3ir7|3ir7]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">narG, bisD, narC, b1224, JW1215 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), narH, b1225, JW1216 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), narI, chlI, b1227, JW1218 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrate_reductase Nitrate reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.99.4 1.7.99.4] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ir6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ir6 OCA], [https://pdbe.org/3ir6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ir6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ir6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ir6 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/NARG_ECOLI NARG_ECOLI]] The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The alpha chain is the actual site of nitrate reduction. [[https://www.uniprot.org/uniprot/NARI_ECOLI NARI_ECOLI]] The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The gamma chain is a membrane-embedded heme-iron unit resembling cytochrome b, which transfers electrons from quinones to the beta subunit. [[https://www.uniprot.org/uniprot/NARH_ECOLI NARH_ECOLI]] The nitrate reductase enzyme complex allows E.coli to use nitrate as an electron acceptor during anaerobic growth. The beta chain is an electron transfer unit containing four cysteine clusters involved in the formation of iron-sulfur centers. Electrons are transferred from the gamma chain to the molybdenum cofactor of the alpha subunit.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ir/3ir6_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3ir6 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We have used site-directed mutagenesis, EPR spectroscopy, redox potentiometry, and protein crystallography to monitor assembly of the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor (Mo-bisPGD) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). Cys and Ser mutants of NarG-His(49) both lack catalytic activity, with only the former assembling FS0 and Mo-bisPGD. Importantly, both prosthetic groups are absent in the NarG-H49S mutant. EPR spectroscopy of the Cys mutant reveals that the E(m) value of the FS0 cluster is decreased by at least 500 mV, preventing its participation in electron transfer to the Mo-bisPGD cofactor. To demonstrate that decreasing the FS0 cluster E(m) results in decreased enzyme activity, we mutated a critical Arg residue (NarG-Arg(94)) in the vicinity of FS0 to a Ser residue. In this case, the E(m) of FS0 is decreased by 115 mV, with a concomitant decrease in enzyme turnover to approximately 30% of the wild type. Analysis of the structure of the NarG-H49S mutant reveals two important aspects of NarGHI maturation: (i) apomolybdo-NarGHI is able to bind GDP moieties at their respective P and Q sites in the absence of the Mo-bisPGD cofactor, and (ii) a critical segment of residues in NarG, (49)HGVNCTG(55), must be correctly positioned to ensure holoenzyme maturation.
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===Crystal structure of NarGHI mutant NarG-H49S===
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Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation.,Rothery RA, Bertero MG, Spreter T, Bouromand N, Strynadka NC, Weiner JH J Biol Chem. 2010 Mar 19;285(12):8801-7. Epub 2010 Jan 6. PMID:20053990<ref>PMID:20053990</ref>
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{{ABSTRACT_PUBMED_20053990}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 3ir6" style="background-color:#fffaf0;"></div>
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[[3ir6]] is a 3 chain structure of [[Nitrate reductase]] with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IR6 OCA].
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==See Also==
==See Also==
*[[Nitrate reductase|Nitrate reductase]]
*[[Nitrate reductase|Nitrate reductase]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:020053990</ref><references group="xtra"/>
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__TOC__
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[[Category: Escherichia coli k-12]]
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</StructureSection>
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[[Category: Ecoli]]
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[[Category: Large Structures]]
[[Category: Nitrate reductase]]
[[Category: Nitrate reductase]]
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[[Category: Bertero, M G.]]
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[[Category: Bertero, M G]]
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[[Category: Rothery, R A.]]
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[[Category: Rothery, R A]]
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[[Category: Strynadka, N C.J.]]
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[[Category: Strynadka, N C.J]]
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[[Category: Weiner, J H.]]
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[[Category: Weiner, J H]]
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[[Category: 3fe-4]]
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[[Category: 4fe-4]]
[[Category: Cell inner membrane]]
[[Category: Cell inner membrane]]
[[Category: Cell membrane]]
[[Category: Cell membrane]]
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[[Category: Molybdenum]]
[[Category: Molybdenum]]
[[Category: Nitrate assimilation]]
[[Category: Nitrate assimilation]]
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[[Category: Nitrate reductase]]
 
[[Category: Oxidoreductase]]
[[Category: Oxidoreductase]]
[[Category: Transmembrane]]
[[Category: Transmembrane]]
[[Category: Transport]]
[[Category: Transport]]

Current revision

Crystal structure of NarGHI mutant NarG-H49S

PDB ID 3ir6

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