1siw

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (00:29, 21 November 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1siw.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of the apomolybdo-NarGHI==
-
|PDB= 1siw |SIZE=350|CAPTION= <scene name='initialview01'>1siw</scene>, resolution 2.20&Aring;
+
<StructureSection load='1siw' size='340' side='right'caption='[[1siw]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=GDP:GUANOSINE-5&#39;-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene> and <scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</scene>
+
<table><tr><td colspan='2'>[[1siw]] is a 3 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=1SIW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SIW FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Nitrate_reductase Nitrate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.99.4 1.7.99.4]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
|GENE= Operon narGHJI: NARG, NARC, BISD, B1224 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), Operon narGHJI: NARH, B1225 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]), Operon narGHJI: NARI, CHLI, B1227 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=1siw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1siw OCA], [https://pdbe.org/1siw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1siw RCSB], [https://www.ebi.ac.uk/pdbsum/1siw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1siw ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[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.
 +
== 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/si/1siw_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=1siw ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We have used EPR spectroscopy, redox potentiometry, and protein crystallography to characterize the [4Fe-4S] cluster (FS0) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). FS0 is clearly visible in the crystal structure of NarGHI [Bertero, M. G., et al. (2003) Nat. Struct. Biol. 10, 681-687] but has novel coordination comprising one His residue and three Cys residues. At low temperatures (&lt;15 K), reduced NarGHI exhibits a previously unobserved EPR signal comprising peaks at g = 5.023 and g = 5.556. We have assigned these features to a [4Fe-4S](+) cluster with an S = (3)/(2) ground state, with the g = 5.023 and g = 5.556 peaks corresponding to subpopulations exhibiting DeltaS = (1)/(2) and DeltaS = (3)/(2) transitions, respectively. Both peaks exhibit midpoint potentials of approximately -55 mV at pH 8.0 and are eliminated in the EPR spectrum of apomolybdo-NarGHI. The structure of apomolybdo-NarGHI reveals that FS0 is still present but that there is significant conformational disorder in a segment of residues that includes one of the Cys ligands. On the basis of these observations, we have assigned the high-spin EPR features of reduced NarGHI to FS0.
-
'''Crystal structure of the apomolybdo-NarGHI'''
+
The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state.,Rothery RA, Bertero MG, Cammack R, Palak M, Blasco F, Strynadka NC, Weiner JH Biochemistry. 2004 May 11;43(18):5324-33. PMID:15122898<ref>PMID:15122898</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1siw" style="background-color:#fffaf0;"></div>
-
==Overview==
+
==See Also==
-
We have used EPR spectroscopy, redox potentiometry, and protein crystallography to characterize the [4Fe-4S] cluster (FS0) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). FS0 is clearly visible in the crystal structure of NarGHI [Bertero, M. G., et al. (2003) Nat. Struct. Biol. 10, 681-687] but has novel coordination comprising one His residue and three Cys residues. At low temperatures (&lt;15 K), reduced NarGHI exhibits a previously unobserved EPR signal comprising peaks at g = 5.023 and g = 5.556. We have assigned these features to a [4Fe-4S](+) cluster with an S = (3)/(2) ground state, with the g = 5.023 and g = 5.556 peaks corresponding to subpopulations exhibiting DeltaS = (1)/(2) and DeltaS = (3)/(2) transitions, respectively. Both peaks exhibit midpoint potentials of approximately -55 mV at pH 8.0 and are eliminated in the EPR spectrum of apomolybdo-NarGHI. The structure of apomolybdo-NarGHI reveals that FS0 is still present but that there is significant conformational disorder in a segment of residues that includes one of the Cys ligands. On the basis of these observations, we have assigned the high-spin EPR features of reduced NarGHI to FS0.
+
*[[Nitrate reductase|Nitrate reductase]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
1SIW is a [[Protein complex]] structure of sequences 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=1SIW OCA].
+
__TOC__
-
 
+
</StructureSection>
-
==Reference==
+
-
The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state., Rothery RA, Bertero MG, Cammack R, Palak M, Blasco F, Strynadka NC, Weiner JH, Biochemistry. 2004 May 11;43(18):5324-33. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15122898 15122898]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Nitrate reductase]]
+
[[Category: Large Structures]]
-
[[Category: Protein complex]]
+
[[Category: Bertero MG]]
-
[[Category: Bertero, M G.]]
+
[[Category: Blasco F]]
-
[[Category: Blasco, F.]]
+
[[Category: Cammack R]]
-
[[Category: Cammack, R.]]
+
[[Category: Palak M]]
-
[[Category: Palak, M.]]
+
[[Category: Rothery RA]]
-
[[Category: Rothery, R A.]]
+
[[Category: Strynadka NC]]
-
[[Category: Strynadka, N C.]]
+
[[Category: Weiner JH]]
-
[[Category: Weiner, J H.]]
+
-
[[Category: 3PH]]
+
-
[[Category: F3S]]
+
-
[[Category: GDP]]
+
-
[[Category: HEM]]
+
-
[[Category: SF4]]
+
-
[[Category: apomolybdo-narghi; electron-transfer; membrane protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 13:37:03 2008''
+

Current revision

Crystal structure of the apomolybdo-NarGHI

PDB ID 1siw

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools