2rdz

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(New page: 200px {{Structure |PDB= 2rdz |SIZE=350|CAPTION= <scene name='initialview01'>2rdz</scene>, resolution 1.740&Aring; |SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+...)
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[[Image:2rdz.jpg|left|200px]]
 
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{{Structure
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==High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.==
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|PDB= 2rdz |SIZE=350|CAPTION= <scene name='initialview01'>2rdz</scene>, resolution 1.740&Aring;
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<StructureSection load='2rdz' size='340' side='right'caption='[[2rdz]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+1501'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+A+1502'>AC2</scene>, <scene name='pdbsite=AC3:Ca+Binding+Site+For+Residue+B+1501'>AC3</scene>, <scene name='pdbsite=AC4:Ca+Binding+Site+For+Residue+B+1502'>AC4</scene>, <scene name='pdbsite=AC5:Ca+Binding+Site+For+Residue+C+1501'>AC5</scene>, <scene name='pdbsite=AC6:Ca+Binding+Site+For+Residue+C+1502'>AC6</scene>, <scene name='pdbsite=AC7:Ca+Binding+Site+For+Residue+D+1501'>AC7</scene>, <scene name='pdbsite=AC8:Ca+Binding+Site+For+Residue+D+1502'>AC8</scene>, <scene name='pdbsite=AC9:So4+Binding+Site+For+Residue+D+2001'>AC9</scene>, <scene name='pdbsite=BC1:So4+Binding+Site+For+Residue+A+2001'>BC1</scene>, <scene name='pdbsite=BC2:So4+Binding+Site+For+Residue+B+2001'>BC2</scene>, <scene name='pdbsite=BC3:So4+Binding+Site+For+Residue+C+2001'>BC3</scene>, <scene name='pdbsite=BC4:Hec+Binding+Site+For+Residue+A+1'>BC4</scene>, <scene name='pdbsite=BC5:Hec+Binding+Site+For+Residue+A+2'>BC5</scene>, <scene name='pdbsite=BC6:Hec+Binding+Site+For+Residue+A+3'>BC6</scene>, <scene name='pdbsite=BC7:Hec+Binding+Site+For+Residue+A+4'>BC7</scene>, <scene name='pdbsite=BC8:Hec+Binding+Site+For+Residue+A+5'>BC8</scene>, <scene name='pdbsite=BC9:Hec+Binding+Site+For+Residue+B+1'>BC9</scene>, <scene name='pdbsite=CC1:Hec+Binding+Site+For+Residue+B+2'>CC1</scene>, <scene name='pdbsite=CC2:Hec+Binding+Site+For+Residue+B+3'>CC2</scene>, <scene name='pdbsite=CC3:Hec+Binding+Site+For+Residue+B+4'>CC3</scene>, <scene name='pdbsite=CC4:Hec+Binding+Site+For+Residue+B+5'>CC4</scene>, <scene name='pdbsite=CC5:Hec+Binding+Site+For+Residue+C+1'>CC5</scene>, <scene name='pdbsite=CC6:Hec+Binding+Site+For+Residue+C+2'>CC6</scene>, <scene name='pdbsite=CC7:Hec+Binding+Site+For+Residue+C+3'>CC7</scene>, <scene name='pdbsite=CC8:Hec+Binding+Site+For+Residue+C+4'>CC8</scene>, <scene name='pdbsite=CC9:Hec+Binding+Site+For+Residue+C+5'>CC9</scene>, <scene name='pdbsite=DC1:Hec+Binding+Site+For+Residue+D+1'>DC1</scene>, <scene name='pdbsite=DC2:Hec+Binding+Site+For+Residue+D+2'>DC2</scene>, <scene name='pdbsite=DC3:Hec+Binding+Site+For+Residue+D+3'>DC3</scene>, <scene name='pdbsite=DC4:Hec+Binding+Site+For+Residue+D+4'>DC4</scene>, <scene name='pdbsite=DC5:Hec+Binding+Site+For+Residue+D+5'>DC5</scene>, <scene name='pdbsite=DC6:Edo+Binding+Site+For+Residue+D+481'>DC6</scene>, <scene name='pdbsite=DC7:Edo+Binding+Site+For+Residue+D+482'>DC7</scene>, <scene name='pdbsite=DC8:Edo+Binding+Site+For+Residue+A+481'>DC8</scene>, <scene name='pdbsite=DC9:Edo+Binding+Site+For+Residue+B+481'>DC9</scene>, <scene name='pdbsite=EC1:Edo+Binding+Site+For+Residue+C+481'>EC1</scene>, <scene name='pdbsite=EC2:Edo+Binding+Site+For+Residue+D+6'>EC2</scene>, <scene name='pdbsite=EC3:Edo+Binding+Site+For+Residue+A+11'>EC3</scene>, <scene name='pdbsite=EC4:Edo+Binding+Site+For+Residue+C+12'>EC4</scene>, <scene name='pdbsite=EC5:Edo+Binding+Site+For+Residue+A+13'>EC5</scene>, <scene name='pdbsite=EC6:Edo+Binding+Site+For+Residue+A+14'>EC6</scene>, <scene name='pdbsite=EC7:Edo+Binding+Site+For+Residue+A+15'>EC7</scene>, <scene name='pdbsite=EC8:Edo+Binding+Site+For+Residue+B+16'>EC8</scene>, <scene name='pdbsite=EC9:Edo+Binding+Site+For+Residue+B+17'>EC9</scene>, <scene name='pdbsite=FC1:Edo+Binding+Site+For+Residue+B+18'>FC1</scene>, <scene name='pdbsite=FC2:Edo+Binding+Site+For+Residue+B+19'>FC2</scene>, <scene name='pdbsite=FC3:Edo+Binding+Site+For+Residue+A+20'>FC3</scene>, <scene name='pdbsite=FC4:Edo+Binding+Site+For+Residue+C+21'>FC4</scene>, <scene name='pdbsite=FC5:Edo+Binding+Site+For+Residue+C+22'>FC5</scene>, <scene name='pdbsite=FC6:Edo+Binding+Site+For+Residue+C+23'>FC6</scene>, <scene name='pdbsite=FC7:Edo+Binding+Site+For+Residue+D+24'>FC7</scene>, <scene name='pdbsite=FC8:Edo+Binding+Site+For+Residue+C+25'>FC8</scene>, <scene name='pdbsite=FC9:Edo+Binding+Site+For+Residue+D+26'>FC9</scene>, <scene name='pdbsite=GC1:Edo+Binding+Site+For+Residue+A+27'>GC1</scene>, <scene name='pdbsite=GC2:Edo+Binding+Site+For+Residue+D+28'>GC2</scene>, <scene name='pdbsite=GC3:Edo+Binding+Site+For+Residue+B+29'>GC3</scene>, <scene name='pdbsite=GC4:Edo+Binding+Site+For+Residue+D+30'>GC4</scene>, <scene name='pdbsite=GC5:Edo+Binding+Site+For+Residue+D+31'>GC5</scene> and <scene name='pdbsite=GC6:Edo+Binding+Site+For+Residue+A+32'>GC6</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[2rdz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDZ FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(cytochrome;_ammonia-forming) Nitrite reductase (cytochrome; ammonia-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.2 1.7.2.2] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.74&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG3303 NrfA]</span>
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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=2rdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdz OCA], [https://pdbe.org/2rdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdz RCSB], [https://www.ebi.ac.uk/pdbsum/2rdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdz ProSAT]</span></td></tr>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdz OCA], [http://www.ebi.ac.uk/pdbsum/2rdz PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2rdz RCSB]</span>
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</table>
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}}
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== Function ==
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[https://www.uniprot.org/uniprot/NRFA_ECOLI NRFA_ECOLI] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182]
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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/rd/2rdz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2rdz 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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The pentaheme cytochrome c nitrite reductase (NrfA) of Escherichia coli is responsible for nitrite reduction during anaerobic respiration when nitrate is scarce. The NrfA active site consists of a hexacoordinate high-spin heme with a lysine ligand on the proximal side and water/hydroxide or substrate on the distal side. There are four further highly conserved active site residues including a glutamine (Q263) positioned 8 A from the heme iron for which the side chain, unusually, coordinates a conserved, essential calcium ion. Mutation of this glutamine to the more usual calcium ligand, glutamate, results in an increase in the K m for nitrite by around 10-fold, while V max is unaltered. Protein film voltammetry showed that lower potentials were required to detect activity from NrfA Q263E when compared with native enzyme, consistent with the introduction of a negative charge into the vicinity of the active site heme. EPR and MCD spectroscopic studies revealed the high spin state of the active site to be preserved, indicating that a water/hydroxide molecule is still coordinated to the heme in the resting state of the enzyme. Comparison of the X-ray crystal structures of the as-prepared, oxidized native and mutant enzymes showed an increased bond distance between the active site heme Fe(III) iron and the distal ligand in the latter as well as changes to the structure and mobility of the active site water molecule network. These results suggest that an important function of the unusual Q263-calcium ion pair is to increase substrate affinity through its role in supporting a network of hydrogen bonded water molecules stabilizing the active site heme distal ligand.
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'''High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.'''
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Role of a Conserved Glutamine Residue in Tuning the Catalytic Activity of Escherichia coli Cytochrome c Nitrite Reductase.,Clarke TA, Kemp GL, Wonderen JH, Doyle RM, Cole JA, Tovell N, Cheesman MR, Butt JN, Richardson DJ, Hemmings AM Biochemistry. 2008 Mar 25;47(12):3789-3799. Epub 2008 Mar 1. PMID:18311941<ref>PMID:18311941</ref>
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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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<div class="pdbe-citations 2rdz" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The pentaheme cytochrome c nitrite reductase (NrfA) of Escherichia coli is responsible for nitrite reduction during anaerobic respiration when nitrate is scarce. The NrfA active site consists of a hexacoordinate high-spin heme with a lysine ligand on the proximal side and water/hydroxide or substrate on the distal side. There are four further highly conserved active site residues including a glutamine (Q263) positioned 8 A from the heme iron for which the side chain, unusually, coordinates a conserved, essential calcium ion. Mutation of this glutamine to the more usual calcium ligand, glutamate, results in an increase in the K m for nitrite by around 10-fold, while V max is unaltered. Protein film voltammetry showed that lower potentials were required to detect activity from NrfA Q263E when compared with native enzyme, consistent with the introduction of a negative charge into the vicinity of the active site heme. EPR and MCD spectroscopic studies revealed the high spin state of the active site to be preserved, indicating that a water/hydroxide molecule is still coordinated to the heme in the resting state of the enzyme. Comparison of the X-ray crystal structures of the as-prepared, oxidized native and mutant enzymes showed an increased bond distance between the active site heme Fe(III) iron and the distal ligand in the latter as well as changes to the structure and mobility of the active site water molecule network. These results suggest that an important function of the unusual Q263-calcium ion pair is to increase substrate affinity through its role in supporting a network of hydrogen bonded water molecules stabilizing the active site heme distal ligand.
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*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
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== References ==
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==About this Structure==
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<references/>
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2RDZ is a [[Single protein]] structure of 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=2RDZ OCA].
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__TOC__
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</StructureSection>
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==Reference==
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Role of a Conserved Glutamine Residue in Tuning the Catalytic Activity of Escherichia coli Cytochrome c Nitrite Reductase., Clarke TA, Kemp GL, Wonderen JH, Doyle RM, Cole JA, Tovell N, Cheesman MR, Butt JN, Richardson DJ, Hemmings AM, Biochemistry. 2008 Mar 25;47(12):3789-3799. Epub 2008 Mar 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18311941 18311941]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Nitrite reductase (cytochrome; ammonia-forming)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Clarke TA]]
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[[Category: Clarke, T A.]]
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[[Category: Hemmings AM]]
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[[Category: Hemmings, A M.]]
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[[Category: RIchardson DJ]]
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[[Category: RIchardson, D J.]]
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[[Category: calcium]]
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[[Category: decaheme]]
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[[Category: electron transport]]
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[[Category: iron]]
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[[Category: metal-binding]]
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[[Category: oxidoreductase]]
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[[Category: periplasm]]
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[[Category: reductase]]
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[[Category: transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 09:53:15 2008''
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Current revision

High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.

PDB ID 2rdz

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