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.


1xx4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:53, 14 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1xx4.jpg|left|200px]]<br /><applet load="1xx4" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1xx4, resolution 2.20&Aring;" />
 
-
'''Crystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA'''<br />
 
-
==Overview==
+
==Crystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA==
-
Two monofunctional Delta(3), Delta(2)-enoyl-CoA isomerases, one in mitochondria (mECI) and the other in both mitochondria and peroxisomes (pECI), belong to the low-similarity isomerase/hydratase superfamily. Both enzymes catalyze the movement of a double bond from C3 to C2 of an unsaturated acyl-CoA substrate for re-entry into the beta-oxidation pathway. Mutagenesis has shown that Glu165 of rat mECI is involved in catalysis; however, the putative catalytic residue in yeast pECI, Glu158, is not conserved in mECI. To elucidate whether Glu165 of mECI is correctly positioned for catalysis, the crystal structure of rat mECI has been solved. Crystal packing suggests the enzyme is trimeric, in contrast to other members of the superfamily, which appear crystallographically to be dimers of trimers. The polypeptide fold of mECI, like pECI, belongs to a subset of this superfamily in which the C-terminal domain of a given monomer interacts with its own N-terminal domain. This differs from that of crotonase and 1,4-dihydroxy-2-naphtoyl-CoA synthase, whose C-terminal domains are involved in domain swapping with an adjacent monomer. The structure confirms Glu165 as the putative catalytic acid/base, positioned to abstract the pro-R proton from C2 and reprotonate at C4 of the acyl chain. The large tunnel-shaped active site cavity observed in the mECI structure explains the relative substrate promiscuity in acyl-chain length and stereochemistry. Comparison with the crystal structure of pECI suggests the catalytic residues from both enzymes are spatially conserved but not in their primary structures, providing a powerful reminder of how catalytic residues cannot be determined solely by sequence alignments.
+
<StructureSection load='1xx4' size='340' side='right'caption='[[1xx4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1xx4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XX4 FirstGlance]. <br>
-
1XX4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=BAM:'>BAM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Dodecenoyl-CoA_isomerase Dodecenoyl-CoA isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.3.8 5.3.3.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XX4 OCA].
+
</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>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xx4 OCA], [https://pdbe.org/1xx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xx4 RCSB], [https://www.ebi.ac.uk/pdbsum/1xx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xx4 ProSAT]</span></td></tr>
-
Domain swapping in the low-similarity isomerase/hydratase superfamily: the crystal structure of rat mitochondrial Delta3, Delta2-enoyl-CoA isomerase., Hubbard PA, Yu W, Schulz H, Kim JJ, Protein Sci. 2005 Jun;14(6):1545-55. Epub 2005 May 9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15883186 15883186]
+
</table>
-
[[Category: Dodecenoyl-CoA isomerase]]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/ECI1_RAT ECI1_RAT] Able to isomerize both 3-cis and 3-trans double bonds into the 2-trans form in a range of enoyl-CoA species.
 +
== 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/xx/1xx4_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1xx4 ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
-
[[Category: Single protein]]
+
[[Category: Hubbard PA]]
-
[[Category: Hubbard, P A.]]
+
[[Category: Kim J-J]]
-
[[Category: Kim, J J.]]
+
[[Category: Schulz H]]
-
[[Category: Schulz, H.]]
+
[[Category: Yu W]]
-
[[Category: Yu, W.]]
+
-
[[Category: BAM]]
+
-
[[Category: PO4]]
+
-
[[Category: ZN]]
+
-
[[Category: crotonase superfamily]]
+
-
[[Category: domain swapped]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:59:32 2008''
+

Current revision

Crystal Structure of Rat Mitochondrial 3,2-Enoyl-CoA

PDB ID 1xx4

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/1xx4"
Personal tools