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1vdh

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Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8

Structural highlights

1vdh is a 5 chain structure with sequence from Thermus thermophilus. 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, TOPSAN

Function

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]^[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 PubMed

The 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

↑ Ebihara A, Okamoto A, Kousumi Y, Yamamoto H, Masui R, Ueyama N, Yokoyama S, Kuramitsu S. Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8. J Struct Funct Genomics. 2005;6(1):21-32. PMID:15965735 doi:10.1007/s10969-005-1103-x
↑ Ebihara A, Okamoto A, Kousumi Y, Yamamoto H, Masui R, Ueyama N, Yokoyama S, Kuramitsu S. Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8. J Struct Funct Genomics. 2005;6(1):21-32. PMID:15965735 doi:10.1007/s10969-005-1103-x

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vdh"

@@ Line 3: / Line 3: @@
 <StructureSection load='1vdh' size='340' side='right'caption='[[1vdh]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1vdh]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VDH FirstGlance]. <br>
+<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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1vdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vdh OCA], [http://pdbe.org/1vdh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1vdh RCSB], [http://www.ebi.ac.uk/pdbsum/1vdh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1vdh ProSAT], [http://www.topsan.org/Proteins/RSGI/1vdh TOPSAN]</span></td></tr>
+</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=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 ==
-[[http://www.uniprot.org/uniprot/Y1714_THET8 Y1714_THET8]] May function as heme-dependent peroxidase. 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, indicating that these are not its natural substrates.<ref>PMID:15965735</ref>
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
 [[Category: Large Structures]]
-[[Category: Ebihara, A]]
+[[Category: Thermus thermophilus]]
-[[Category: Inoue, Y]]
+[[Category: Ebihara A]]
-[[Category: Kousumi, Y]]
+[[Category: Inoue Y]]
-[[Category: Kuramitsu, S]]
+[[Category: Kousumi Y]]
-[[Category: Masui, R]]
+[[Category: Kuramitsu S]]
-[[Category: Okamoto, A]]
+[[Category: Masui R]]
-[[Category: Structural genomic]]
+[[Category: Okamoto A]]
-[[Category: Shibata, T]]
+[[Category: Shibata T]]
-[[Category: Ueyama, N]]
+[[Category: Ueyama N]]
-[[Category: Yamamoto, H]]
+[[Category: Yamamoto H]]
-[[Category: Yokoyama, S]]
+[[Category: Yokoyama S]]
-[[Category: Beta barrel]]
-[[Category: Rsgi]]
-[[Category: Unknown function]]

1vdh

From Proteopedia

Current revision

Structure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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