1vdh
From Proteopedia
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==Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8== | ==Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8== | ||
| - | <StructureSection load='1vdh' size='340' side='right' caption='[[1vdh]], [[Resolution|resolution]] 2.00Å' scene=''> | + | <StructureSection load='1vdh' size='340' side='right'caption='[[1vdh]], [[Resolution|resolution]] 2.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1vdh]] is a 5 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[1vdh]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VDH FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | <table> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vdh OCA], [https://pdbe.org/1vdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vdh RCSB], [https://www.ebi.ac.uk/pdbsum/1vdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vdh ProSAT], [https://www.topsan.org/Proteins/RSGI/1vdh TOPSAN]</span></td></tr> |
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/CHDC_THET8 CHDC_THET8] Involved in coproporphyrin-dependent heme b biosynthesis. Catalyzes the decarboxylation of Fe-coproporphyrin III (coproheme) to heme b (protoheme IX), the last step of the pathway. The reaction occurs in a stepwise manner with a three-propionate harderoheme intermediate (By similarity). When reconstituted with heme, can generate oxygen using chlorite or hydrogen peroxide as substrate (in vitro), but has very low affinity for hydrogen peroxide and chlorite and extremely low enzyme activity (PubMed:15965735).[HAMAP-Rule:MF_01442]<ref>PMID:15965735</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vd/1vdh_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vd/1vdh_consurf.spt"</scriptWhenChecked> |
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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=1vdh ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
| + | <div class="pdbe-citations 1vdh" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
| - | [[Category: Ebihara | + | [[Category: Ebihara A]] |
| - | [[Category: Inoue | + | [[Category: Inoue Y]] |
| - | [[Category: Kousumi | + | [[Category: Kousumi Y]] |
| - | [[Category: Kuramitsu | + | [[Category: Kuramitsu S]] |
| - | [[Category: Masui | + | [[Category: Masui R]] |
| - | [[Category: Okamoto | + | [[Category: Okamoto A]] |
| - | + | [[Category: Shibata T]] | |
| - | [[Category: Shibata | + | [[Category: Ueyama N]] |
| - | [[Category: Ueyama | + | [[Category: Yamamoto H]] |
| - | [[Category: Yamamoto | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama | + | |
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Current revision
Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8
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Categories: Large Structures | Thermus thermophilus | Ebihara A | Inoue Y | Kousumi Y | Kuramitsu S | Masui R | Okamoto A | Shibata T | Ueyama N | Yamamoto H | Yokoyama S
