3gvq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:13, 6 September 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3gvq.jpg|left|200px]]
 
-
<!--
+
==UROD single-chain dimer==
-
The line below this paragraph, containing "STRUCTURE_3gvq", creates the "Structure Box" on the page.
+
<StructureSection load='3gvq' size='340' side='right'caption='[[3gvq]], [[Resolution|resolution]] 2.10&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'>[[3gvq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GVQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GVQ 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]] 2.1&#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=3gvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gvq OCA], [https://pdbe.org/3gvq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gvq RCSB], [https://www.ebi.ac.uk/pdbsum/3gvq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gvq ProSAT]</span></td></tr>
-
{{STRUCTURE_3gvq| PDB=3gvq | SCENE= }}
+
</table>
 +
== Disease ==
 +
[https://www.uniprot.org/uniprot/DCUP_HUMAN DCUP_HUMAN] Defects in UROD are the cause of familial porphyria cutanea tarda (FPCT) [MIM:[https://omim.org/entry/176100 176100]; also known as porphyria cutanea tarda type II. FPCT is an autosomal dominant disorder characterized by light-sensitive dermatitis, with onset in later life. It is associated with the excretion of large amounts of uroporphyrin in the urine. Iron overload is often present in association with varying degrees of liver damage. Besides the familial form of PCT, a relatively common idiosyncratic form is known in which only the liver enzyme is reduced. This form is referred to as porphyria cutanea tarda "sporadic" type or type I [MIM:[https://omim.org/entry/176090 176090]. PCT type I occurs sporadically as an unusual accompaniment of common hepatic disorders such as alcohol-associated liver disease.<ref>PMID:2243121</ref> <ref>PMID:11719352</ref> <ref>PMID:2920211</ref> <ref>PMID:7706766</ref> <ref>PMID:8896428</ref> <ref>PMID:9792863</ref> <ref>PMID:10338097</ref> <ref>PMID:10477430</ref> <ref>PMID:11069625</ref> <ref>PMID:11295834</ref> Defects in UROD are the cause of hepatoerythropoietic porphyria (HEP) [MIM:[https://omim.org/entry/176100 176100]. HEP is a rare autosomal recessive disorder. It is the severe form of cutaneous porphyria, and presents in infancy. The level of UROD is very low in erythrocytes and cultured skin fibroblasts, suggesting that HEP is the homozygous state for porphyria cutanea tarda.<ref>PMID:8896428</ref> <ref>PMID:8644733</ref> <ref>PMID:3775362</ref> <ref>PMID:1905636</ref> <ref>PMID:1634232</ref> <ref>PMID:8176248</ref> <ref>PMID:12071824</ref> <ref>PMID:15491440</ref> <ref>PMID:17240319</ref> <ref>PMID:21668429</ref>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/DCUP_HUMAN DCUP_HUMAN] Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III.
 +
== 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/gv/3gvq_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=3gvq ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Uroporphyrinogen decarboxylase (URO-D; EC 4.1.1.37), the fifth enzyme of the heme biosynthetic pathway, is required for the production of heme, vitamin B12, siroheme, and chlorophyll precursors. URO-D catalyzes the sequential decarboxylation of four acetate side chains in the pyrrole groups of uroporphyrinogen to produce coproporphyrinogen. URO-D is a stable homodimer, with the active-site clefts of the two subunits adjacent to each other. It has been hypothesized that the two catalytic centers interact functionally, perhaps by shuttling of reaction intermediates between subunits. We tested this hypothesis by construction of a single-chain protein (single-chain URO-D) in which the two subunits were connected by a flexible linker. The crystal structure of this protein was shown to be superimposable with wild-type activity and to have comparable catalytic activity. Mutations that impaired one or the other of the two active sites of single-chain URO-D resulted in approximately half of wild-type activity. The distributions of reaction intermediates were the same for mutant and wild-type sequences and were unaltered in a competition experiment using I and III isomer substrates. These observations indicate that communication between active sites is not required for enzyme function and suggest that the dimeric structure of URO-D is required to achieve conformational stability and to create a large active-site cleft.
-
===UROD single-chain dimer===
+
Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen.,Phillips JD, Warby CA, Whitby FG, Kushner JP, Hill CP J Mol Biol. 2009 Jun 5;389(2):306-14. Epub 2009 Apr 10. PMID:19362562<ref>PMID:19362562</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_19362562}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 3gvq" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 19362562 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_19362562}}
+
__TOC__
-
 
+
</StructureSection>
-
==Disease==
+
-
Known disease associated with this structure: Porphyria cutanea tarda OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176100 176100]], Porphyria, hepatoerythropoietic OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176100 176100]]
+
-
 
+
-
==About this Structure==
+
-
3GVQ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GVQ OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:19362562</ref><references group="xtra"/>
+
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Uroporphyrinogen decarboxylase]]
+
[[Category: Large Structures]]
-
[[Category: Hill, C P.]]
+
[[Category: Hill CP]]
-
[[Category: Kushner, J P.]]
+
[[Category: Kushner JP]]
-
[[Category: Phillips, J D.]]
+
[[Category: Phillips JD]]
-
[[Category: Warby, C.]]
+
[[Category: Warby C]]
-
[[Category: Whitby, F G.]]
+
[[Category: Whitby FG]]
-
[[Category: Acetylation]]
+
-
[[Category: Alpha-8-beta-8 barrel]]
+
-
[[Category: Cytoplasm]]
+
-
[[Category: Decarboxylase]]
+
-
[[Category: Disease mutation]]
+
-
[[Category: Heme]]
+
-
[[Category: Heme biosynthesis]]
+
-
[[Category: Lyase]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Porphyrin biosynthesis]]
+
-
[[Category: Uroporphyrinogen]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 8 09:29:06 2009''
+

Current revision

UROD single-chain dimer

PDB ID 3gvq

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools