3i6d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:27, 20 March 2024) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
-
{{STRUCTURE_3i6d| PDB=3i6d | SCENE= }}
 
-
===Crystal structure of PPO from bacillus subtilis with AF===
 
-
{{ABSTRACT_PUBMED_19944166}}
 
-
==Function==
+
==Crystal structure of PPO from bacillus subtilis with AF==
-
[[http://www.uniprot.org/uniprot/PPOX_BACSU PPOX_BACSU]] Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX. Also oxidizes the pathway intermediate coproporphyrinogen-III.
+
<StructureSection load='3i6d' size='340' side='right'caption='[[3i6d]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[3i6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I6D FirstGlance]. <br>
-
[[3i6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I6D 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]] 2.9&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACJ:5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC+ACID'>ACJ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3i6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i6d OCA], [https://pdbe.org/3i6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i6d RCSB], [https://www.ebi.ac.uk/pdbsum/3i6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i6d ProSAT]</span></td></tr>
-
<ref group="xtra">PMID:019944166</ref><references group="xtra"/><references/>
+
</table>
-
[[Category: Bacillus globigii migula 1900]]
+
== Function ==
-
[[Category: Protoporphyrinogen oxidase]]
+
[https://www.uniprot.org/uniprot/CGOX_BACSU CGOX_BACSU] Involved in coproporphyrin-dependent heme b biosynthesis (PubMed:7928957, PubMed:9217019). Catalyzes the oxidation of coproporphyrinogen III to coproporphyrin III (PubMed:8288631, PubMed:7928957, PubMed:9217019, PubMed:9784236). Can also oxidize protoporphyrinogen IX to protoporphyrin-IX (PubMed:8288631, PubMed:7928957, PubMed:9217019, PubMed:9784236, PubMed:19944166). The specific activity for the oxidation of coproporphyrinogen III is much higher than that for the oxidation of protoporphyrinogen IX (PubMed:7928957, PubMed:9217019). Can also oxidize mesoporphyrinogen IX, but not uroporphyrinogen III (PubMed:8288631, PubMed:9784236, PubMed:7928957).<ref>PMID:19944166</ref> <ref>PMID:7928957</ref> <ref>PMID:8288631</ref> <ref>PMID:9217019</ref> <ref>PMID:9784236</ref>
-
[[Category: Shen, Y.]]
+
== Evolutionary Conservation ==
-
[[Category: Fad]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Flavoprotein]]
+
Check<jmol>
-
[[Category: Oxidoreductase]]
+
<jmolCheckbox>
-
[[Category: Porphyrin biosynthesis]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i6/3i6d_consurf.spt"</scriptWhenChecked>
-
[[Category: Protein-inhibitor complex]]
+
<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=3i6d ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Bacillus subtilis]]
 +
[[Category: Large Structures]]
 +
[[Category: Shen Y]]

Current revision

Crystal structure of PPO from bacillus subtilis with AF

PDB ID 3i6d

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/3i6d"
Personal tools