This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1oqb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:28, 13 March 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1oqb.gif|left|200px]]
 
-
<!--
+
==The Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).==
-
The line below this paragraph, containing "STRUCTURE_1oqb", creates the "Structure Box" on the page.
+
<StructureSection load='1oqb' size='340' side='right'caption='[[1oqb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1oqb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OQB FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
-
{{STRUCTURE_1oqb| PDB=1oqb | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oqb OCA], [https://pdbe.org/1oqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oqb RCSB], [https://www.ebi.ac.uk/pdbsum/1oqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oqb ProSAT]</span></td></tr>
-
 
+
</table>
-
'''The Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/STAD_RICCO STAD_RICCO] Converts stearoyl-ACP to oleoyl-ACP by introduction of a cis double bond between carbons Delta(9) and Delta(10) of the acyl chain.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
Delta9 stearoyl-acyl carrier protein (ACP) desaturase is a mu-oxo-bridged di-iron enzyme, which belongs to the structural class I of large helix bundle proteins and that catalyzes the NADPH and O2-dependent formation of a cis-double bond in stearoyl-ACP. The crystal structures of complexes with azide and acetate, respectively, as well as the apoand single-iron forms of Delta9 stearoyl-ACP desaturase from Ricinus communis have been determined. In the azide complex, the ligand forms a mu-1,3-bridge between the two iron ions in the active site, replacing a loosely bound water molecule. The structure of the acetate complex is similar, with acetate bridging the di-iron center in the same orientation with respect to the di-iron center. However, in this complex, the iron ligand Glu196 has changed its coordination mode from bidentate to monodentate, the first crystallographic observation of a carboxylate shift in Delta9 stearoyl-ACP desaturase. The two complexes are proposed to mimic a mu-1,2 peroxo intermediate present during catalytic turnover. There are striking structural similarities between the di-iron center in the Delta9 stearoyl-ACP desaturase-azide complex and in the reduced rubrerythrin-azide complex. This suggests that Delta9 stearoyl-ACP desaturase might catalyze the formation of water from exogenous hydrogen peroxide at a low rate. From the similarity in iron center structure, we propose that the mu-oxo-bridge in oxidized desaturase is bound to the di-iron center as in rubrerythrin and not as reported for the R2 subunit of ribonucleotide reductase and the hydroxylase subunit of methane monooxygenase. The crystal structure of the one-iron depleted desaturase species demonstrates that the affinities for the two iron ions comprising the di-iron center are not equivalent, Fe1 being the higher affinity site and Fe2 being the lower affinity site.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oq/1oqb_consurf.spt"</scriptWhenChecked>
-
1OQB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Ricinus_communis Ricinus communis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OQB OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates., Moche M, Shanklin J, Ghoshal A, Lindqvist Y, J Biol Chem. 2003 Jul 4;278(27):25072-80. Epub 2003 Apr 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12704186 12704186]
+
</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=1oqb ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Ricinus communis]]
[[Category: Ricinus communis]]
-
[[Category: Single protein]]
+
[[Category: Ghoshal AK]]
-
[[Category: Ghoshal, A K.]]
+
[[Category: Lindqvist Y]]
-
[[Category: Lindqvist, Y.]]
+
[[Category: Moche M]]
-
[[Category: Moche, M.]]
+
[[Category: Shanklin J]]
-
[[Category: Shanklin, J.]]
+
-
[[Category: Di-iron enzyme]]
+
-
[[Category: Electron transfer]]
+
-
[[Category: Fatty acid biosynthesis]]
+
-
[[Category: Four-helix bundle]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 04:09:19 2008''
+

Current revision

The Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier Protein Desaturase from Ricinus Communis (Castor Bean).

PDB ID 1oqb

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1oqb"
Personal tools