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| | ==Structure of the E. coli C-P lyase core complex== | | ==Structure of the E. coli C-P lyase core complex== |
| - | <StructureSection load='4xb6' size='340' side='right' caption='[[4xb6]], [[Resolution|resolution]] 1.70Å' scene=''> | + | <StructureSection load='4xb6' size='340' side='right'caption='[[4xb6]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4xb6]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XB6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4xb6]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XB6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.7Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alpha-D-ribose_1-methylphosphonate_5-triphosphate_synthase Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.8.37 2.7.8.37] </span></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=4xb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xb6 OCA], [https://pdbe.org/4xb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xb6 RCSB], [https://www.ebi.ac.uk/pdbsum/4xb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xb6 ProSAT]</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=4xb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xb6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xb6 RCSB], [http://www.ebi.ac.uk/pdbsum/4xb6 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PHNJ_ECOLI PHNJ_ECOLI]] Catalyzes the breakage of the C-P bond in alpha-D-ribose 1-methylphosphonate 5-phosphate (PRPn) forming alpha-D-ribose 1,2-cyclic phosphate 5-phosphate (PRcP).<ref>PMID:22089136</ref> [[http://www.uniprot.org/uniprot/PHNG_ECOLI PHNG_ECOLI]] Together with PhnH, PhnI and PhnL is required for the transfer of the ribose triphosphate moiety from ATP to methyl phosphonate.<ref>PMID:22089136</ref> [[http://www.uniprot.org/uniprot/PHNI_ECOLI PHNI_ECOLI]] Together with PhnG, PhnH and PhnL is required for the transfer of the ribose triphosphate moiety from ATP to methyl phosphonate. PhnI alone has nucleosidase activity, catalyzing the hydrolysis of ATP or GTP forming alpha-D-ribose 5-triphosphate and adenine or guanine, respectively.<ref>PMID:22089136</ref> [[http://www.uniprot.org/uniprot/PHNH_ECOLI PHNH_ECOLI]] Together with PhnG, PhnI and PhnL is required for the transfer of the ribose triphosphate moiety from ATP to methyl phosphonate.<ref>PMID:22089136</ref> | + | [https://www.uniprot.org/uniprot/PHNG_ECOLI PHNG_ECOLI] Together with PhnH, PhnI and PhnL is required for the transfer of the ribose triphosphate moiety from ATP to methyl phosphonate.<ref>PMID:22089136</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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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 4xb6" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase]] | + | [[Category: Escherichia coli str. K-12 substr. MG1655]] |
| - | [[Category: Brodersen, D E]] | + | [[Category: Large Structures]] |
| - | [[Category: Protein complex]] | + | [[Category: Brodersen DE]] |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
PHNG_ECOLI Together with PhnH, PhnI and PhnL is required for the transfer of the ribose triphosphate moiety from ATP to methyl phosphonate.[1]
Publication Abstract from PubMed
Phosphorus is required for all life and microorganisms can extract it from their environment through several metabolic pathways. When phosphate is in limited supply, some bacteria are able to use phosphonate compounds, which require specialized enzymatic machinery to break the stable carbon-phosphorus (C-P) bond. Despite its importance, the details of how this machinery catabolizes phosphonates remain unknown. Here we determine the crystal structure of the 240-kilodalton Escherichia coli C-P lyase core complex (PhnG-PhnH-PhnI-PhnJ; PhnGHIJ), and show that it is a two-fold symmetric hetero-octamer comprising an intertwined network of subunits with unexpected self-homologies. It contains two potential active sites that probably couple phosphonate compounds to ATP and subsequently hydrolyse the C-P bond. We map the binding site of PhnK on the complex using electron microscopy, and show that it binds to a conserved insertion domain of PhnJ. Our results provide a structural basis for understanding microbial phosphonate breakdown.
Structural insights into the bacterial carbon-phosphorus lyase machinery.,Seweryn P, Van LB, Kjeldgaard M, Russo CJ, Passmore LA, Hove-Jensen B, Jochimsen B, Brodersen DE Nature. 2015 Aug 17. doi: 10.1038/nature14683. PMID:26280334[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kamat SS, Williams HJ, Raushel FM. Intermediates in the transformation of phosphonates to phosphate by bacteria. Nature. 2011 Nov 16;480(7378):570-3. doi: 10.1038/nature10622. PMID:22089136 doi:http://dx.doi.org/10.1038/nature10622
- ↑ Seweryn P, Van LB, Kjeldgaard M, Russo CJ, Passmore LA, Hove-Jensen B, Jochimsen B, Brodersen DE. Structural insights into the bacterial carbon-phosphorus lyase machinery. Nature. 2015 Aug 17. doi: 10.1038/nature14683. PMID:26280334 doi:http://dx.doi.org/10.1038/nature14683
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