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| | ==Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus== | | ==Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus== |
| - | <StructureSection load='2dj5' size='340' side='right' caption='[[2dj5]], [[Resolution|resolution]] 2.55Å' scene=''> | + | <StructureSection load='2dj5' size='340' side='right'caption='[[2dj5]], [[Resolution|resolution]] 2.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dj5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DJ5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dj5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DJ5 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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]] 2.55Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tjn|1tjn]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbiX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2234 ARCFL])</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=2dj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dj5 OCA], [https://pdbe.org/2dj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dj5 RCSB], [https://www.ebi.ac.uk/pdbsum/2dj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dj5 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Sirohydrochlorin_cobaltochelatase Sirohydrochlorin cobaltochelatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.3 4.99.1.3] </span></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=2dj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dj5 OCA], [http://pdbe.org/2dj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dj5 RCSB], [http://www.ebi.ac.uk/pdbsum/2dj5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dj5 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CBIX_ARCFU CBIX_ARCFU]] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis.<ref>PMID:16835730</ref> | + | [https://www.uniprot.org/uniprot/CBIX_ARCFU CBIX_ARCFU] Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis.<ref>PMID:16835730</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/dj/2dj5_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dj/2dj5_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> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arcfl]] | + | [[Category: Archaeoglobus fulgidus]] |
| - | [[Category: Sirohydrochlorin cobaltochelatase]] | + | [[Category: Large Structures]] |
| - | [[Category: Cherney, M M]] | + | [[Category: Cherney MM]] |
| - | [[Category: James, M N.G]] | + | [[Category: James MNG]] |
| - | [[Category: Yin, J]] | + | [[Category: Yin J]] |
| - | [[Category: Beta-alpha-beta]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Parallel beta sheet]]
| + | |
| Structural highlights
Function
CBIX_ARCFU Catalyzes the insertion of Co(2+) into sirohydrochlorin as part of the anaerobic pathway to cobalamin biosynthesis.[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 Archaeoglobus fulgidus gene af0721 encodes CbiX(S), a small cobaltochelatase associated with the anaerobic biosynthesis of vitamin B12 (cobalamin). The protein was shown to have activity both in vivo and in vitro, catalyzing the insertion of Co2+ into sirohydrochlorin. The structure of CbiX(S) was determined in two different crystal forms and was shown to consist of a central mixed beta-sheet flanked by four alpha-helices, one of which originates in the C-terminus of a neighboring molecule. CbiX(S) is about half the size of other Class II tetrapyrrole chelatases. The overall topography of CbiX(S) exhibits substantial resemblance to both the N- and C-terminal regions of several members of the Class II metal chelatases involved in tetrapyrrole biosynthesis. Two histidines (His10 and His74), are in similar positions as the catalytic histidine residues in the anaerobic cobaltochelatase CbiK (His145 and His207). In light of the hypothesis that suggests the larger chelatases evolved via gene duplication and fusion from a CbiX(S)-like enzyme, the structure of AF0721 may represent that of an "ancestral" precursor of class II metal chelatases.
Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus.,Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN J Struct Funct Genomics. 2006 Mar;7(1):37-50. Epub 2006 Jul 12. PMID:16835730[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN. Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus. J Struct Funct Genomics. 2006 Mar;7(1):37-50. Epub 2006 Jul 12. PMID:16835730 doi:10.1007/s10969-006-9008-x
- ↑ Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN. Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus. J Struct Funct Genomics. 2006 Mar;7(1):37-50. Epub 2006 Jul 12. PMID:16835730 doi:10.1007/s10969-006-9008-x
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