Proteopedia

1gu6: Difference between revisions

← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1gu6.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_1gu6", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_1gu6|  PDB=1gu6  |  SCENE=  }}
'''STRUCTURE OF THE PERIPLASMIC CYTOCHROME C NITRITE REDUCTASE FROM ESCHERICHIA COLI'''


==Structure of the Periplasmic Cytochrome c Nitrite Reductase from Escherichia coli==
<StructureSection load='1gu6' size='340' side='right'caption='[[1gu6]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1gu6]] 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=1GU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GU6 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gu6 OCA], [https://pdbe.org/1gu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gu6 RCSB], [https://www.ebi.ac.uk/pdbsum/1gu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gu6 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NRFA_ECOLI NRFA_ECOLI] Plays a role in nitrite reduction.[HAMAP-Rule:MF_01182]
== 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/gu/1gu6_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1gu6 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure and spectroscopic properties of the periplasmic penta-heme cytochrome c nitrite reductase (NrfA) of Escherichia coli are presented. The structure is the first for a member of the NrfA subgroup that utilize a soluble penta-heme cytochrome, NrfB, as a redox partner. Comparison to the structures of Wolinella succinogenes NrfA and Sulfospirillum deleyianum NrfA, which accept electrons from a membrane-anchored tetra-heme cytochrome (NrfH), reveals notable differences in the protein surface around heme 2, which may be the docking site for the redox partner. The structure shows that four of the NrfA hemes (hemes 2-5) have bis-histidine axial heme-Fe ligation. The catalytic heme-Fe (heme 1) has a lysine distal ligand and an oxygen atom proximal ligand. Analysis of NrfA in solution by magnetic circular dichroism (MCD) suggested that the oxygen ligand arose from water. Electron paramagnetic resonance (EPR) spectra were collected from electrochemically poised NrfA samples. Broad perpendicular mode signals at g similar 10.8 and 3.5, characteristic of weakly spin-coupled S = 5/2, S = 1/2 paramagnets, titrated with E(m) = -107 mV. A possible origin for these are the active site Lys-OH(2) coordinated heme (heme 1) and a nearby bis-His coordinated heme (heme 3). A rhombic heme Fe(III) EPR signal at g(z) = 2.91, g(y) = 2.3, g(x) = 1.5 titrated with E(m) = -37 mV and is likely to arise from bis-His coordinated heme (heme 2) in which the interplanar angle of the imidazole rings is 21.2. The final two bis-His coordinated hemes (hemes 4 and 5) have imidazole interplanar angles of 64.4 and 71.8. Either, or both, of these hemes could give rise to a "Large g max" EPR signal at g(z)() = 3.17 that titrated at potentials between -250 and -400 mV. Previous spectroscopic studies on NrfA from a number of bacterial species are considered in the light of the structure-based spectro-potentiometric analysis presented for the E. coli NrfA.


==Overview==
Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli.,Bamford VA, Angove HC, Seward HE, Thomson AJ, Cole JA, Butt JN, Hemmings AM, Richardson DJ Biochemistry. 2002 Mar 5;41(9):2921-31. PMID:11863430<ref>PMID:11863430</ref>
The crystal structure and spectroscopic properties of the periplasmic penta-heme cytochrome c nitrite reductase (NrfA) of Escherichia coli are presented. The structure is the first for a member of the NrfA subgroup that utilize a soluble penta-heme cytochrome, NrfB, as a redox partner. Comparison to the structures of Wolinella succinogenes NrfA and Sulfospirillum deleyianum NrfA, which accept electrons from a membrane-anchored tetra-heme cytochrome (NrfH), reveals notable differences in the protein surface around heme 2, which may be the docking site for the redox partner. The structure shows that four of the NrfA hemes (hemes 2-5) have bis-histidine axial heme-Fe ligation. The catalytic heme-Fe (heme 1) has a lysine distal ligand and an oxygen atom proximal ligand. Analysis of NrfA in solution by magnetic circular dichroism (MCD) suggested that the oxygen ligand arose from water. Electron paramagnetic resonance (EPR) spectra were collected from electrochemically poised NrfA samples. Broad perpendicular mode signals at g similar 10.8 and 3.5, characteristic of weakly spin-coupled S = 5/2, S = 1/2 paramagnets, titrated with E(m) = -107 mV. A possible origin for these are the active site Lys-OH(2) coordinated heme (heme 1) and a nearby bis-His coordinated heme (heme 3). A rhombic heme Fe(III) EPR signal at g(z) = 2.91, g(y) = 2.3, g(x) = 1.5 titrated with E(m) = -37 mV and is likely to arise from bis-His coordinated heme (heme 2) in which the interplanar angle of the imidazole rings is 21.2. The final two bis-His coordinated hemes (hemes 4 and 5) have imidazole interplanar angles of 64.4 and 71.8. Either, or both, of these hemes could give rise to a "Large g max" EPR signal at g(z)() = 3.17 that titrated at potentials between -250 and -400 mV. Previous spectroscopic studies on NrfA from a number of bacterial species are considered in the light of the structure-based spectro-potentiometric analysis presented for the E. coli NrfA.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1GU6 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=1GU6 OCA].
</div>
<div class="pdbe-citations 1gu6" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structure and spectroscopy of the periplasmic cytochrome c nitrite reductase from Escherichia coli., Bamford VA, Angove HC, Seward HE, Thomson AJ, Cole JA, Butt JN, Hemmings AM, Richardson DJ, Biochemistry. 2002 Mar 5;41(9):2921-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11863430 11863430]
*[[Cytochrome c nitrite reductase|Cytochrome c nitrite reductase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Angove, H C.]]
[[Category: Angove HC]]
[[Category: Bamford, V A.]]
[[Category: Bamford VA]]
[[Category: Butt, J N.]]
[[Category: Butt JN]]
[[Category: Cole, J A.]]
[[Category: Cole JA]]
[[Category: Hemmings, A M.]]
[[Category: Hemmings AM]]
[[Category: Richardson, D J.]]
[[Category: Richardson DJ]]
[[Category: Seward, H E.]]
[[Category: Seward HE]]
[[Category: Thomson, A J.]]
[[Category: Thomson AJ]]
[[Category: Anaerobic nitrite respiration]]
[[Category: C-type cytochrome]]
[[Category: Periplasmic nitrite reductase]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 18:00:47 2008''

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/w/1gu6"