1tkl: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1tkl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tkl, resolution 2.00Å" /> '''Yeast Oxygen-Depende...
 
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1tkl.jpg|left|200px]]<br /><applet load="1tkl" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1tkl, resolution 2.00&Aring;" />
'''Yeast Oxygen-Dependent Coproporphyrinogen Oxidase'''<br />


==Overview==
==Yeast Oxygen-Dependent Coproporphyrinogen Oxidase==
Coproporphyrinogen oxidase (CPO) is an essential enzyme that catalyzes the, sixth step of the heme biosynthetic pathway. Unusually for heme, biosynthetic enzymes, CPO exists in two evolutionarily and mechanistically, distinct families, with eukaryotes and some prokaryotes employing members, of the highly conserved oxygen-dependent CPO family. Here, we report the, crystal structure of the oxygen-dependent CPO from Saccharomyces, cerevisiae (Hem13p), which was determined by optimized sulfur anomalous, scattering and refined to a resolution of 2.0 A. The protein adopts a, novel structure that is quite different from predicted models and features, a central flat seven-stranded anti-parallel sheet that is flanked by, helices. The dimeric assembly, which is seen in different crystal forms, is formed by packing of helices and a short isolated strand that forms a, beta-ladder with its counterpart in the partner subunit. The deep, active-site cleft is lined by conserved residues and has been captured in, open and closed conformations in two different crystal forms. A, substratesized cavity is completely buried in the closed conformation by, the approximately 8-A movement of a helix that forms a lid over the active, site. The structure therefore suggests residues that likely play critical, roles in catalysis and explains the deleterious effect of many of the, mutations associated with the disease hereditary coproporphyria.
<StructureSection load='1tkl' size='340' side='right'caption='[[1tkl]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1tkl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKL FirstGlance]. <br>
1TKL is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Active as [http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TKL 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&#8491;</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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [https://pdbe.org/1tkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [https://www.ebi.ac.uk/pdbsum/1tkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkl ProSAT]</span></td></tr>
==Reference==
</table>
Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae., Phillips JD, Whitby FG, Warby CA, Labbe P, Yang C, Pflugrath JW, Ferrara JD, Robinson H, Kushner JP, Hill CP, J Biol Chem. 2004 Sep 10;279(37):38960-8. Epub 2004 Jun 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15194705 15194705]
== Function ==
[[Category: Coproporphyrinogen oxidase]]
[https://www.uniprot.org/uniprot/HEM6_YEAST HEM6_YEAST] Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX (By similarity).
== 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/tk/1tkl_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=1tkl ConSurf].
<div style="clear:both"></div>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Ferrara JD]]
[[Category: Ferrara, J.D.]]
[[Category: Hill CP]]
[[Category: Hill, C.P.]]
[[Category: Kushner JP]]
[[Category: Kushner, J.P.]]
[[Category: Labbe P]]
[[Category: Labbe, P.]]
[[Category: Pflugrath JW]]
[[Category: Pflugrath, J.W.]]
[[Category: Phillips JD]]
[[Category: Phillips, J.D.]]
[[Category: Robinson H]]
[[Category: Robinson, H.]]
[[Category: Warby CA]]
[[Category: Warby, C.A.]]
[[Category: Whitby FG]]
[[Category: Whitby, F.G.]]
[[Category: Yang C]]
[[Category: Yang, C.]]
[[Category: coproporphyrinogen oxidase]]
[[Category: enzyme]]
[[Category: heme biosynthesis]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 03:21:29 2007''

Latest revision as of 11:40, 14 February 2024

Yeast Oxygen-Dependent Coproporphyrinogen OxidaseYeast Oxygen-Dependent Coproporphyrinogen Oxidase

Structural highlights

1tkl is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HEM6_YEAST Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1tkl, resolution 2.00Å

Drag the structure with the mouse to rotate

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

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1tkl&oldid=4055585"