1vdh: Difference between revisions
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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 id='resources'><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> | ||
<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> | </table> | ||
== Function == | == 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 | |||
Latest revision as of 03:01, 28 December 2023
Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8
Structural highlights
FunctionCHDC_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][1] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe TT1485 gene from Thermus thermophilus HB8 encodes a hypothetical protein of unknown function with about 20 sequence homologs of bacterial or archaeal origin. Together they form a family of uncharacterized proteins, the cluster of orthologous group COG3253. Using a combination of amino acid sequence analysis, three-dimensional structural studies and biochemical assays, we identified TT1485 as a novel heme-binding protein. The crystal structure reveals that this protein is a pentamer and each monomer exhibits a beta-barrel fold. TT1485 is structurally similar to muconolactone isomerase, but this provided no functional clues. Amino acid sequence analysis revealed remote homology to a heme enzyme, chlorite dismutase. Strikingly, amino acid residues that are highly conserved in the homologous hypothetical proteins and chlorite dismutase cluster around a deep cavity on the surface of each monomer. Molecular modeling shows that the cavity can accommodate a heme group with a strictly conserved His as a heme ligand. TT1485 reconstituted with iron protoporphyrin IX chloride gave a low chlorite dismutase activity, indicating that TT1485 catalyzes a reaction other than chlorite degradation. The presence of a possible Fe-His-Asp triad in the heme proximal site suggests that TT1485 functions as a novel heme peroxidase to detoxify hydrogen peroxide within the cell. Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8.,Ebihara A, Okamoto A, Kousumi Y, Yamamoto H, Masui R, Ueyama N, Yokoyama S, Kuramitsu S J Struct Funct Genomics. 2005;6(1):21-32. PMID:15965735[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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