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| | <StructureSection load='6pd1' size='340' side='right'caption='[[6pd1]], [[Resolution|resolution]] 2.72Å' scene=''> | | <StructureSection load='6pd1' size='340' side='right'caption='[[6pd1]], [[Resolution|resolution]] 2.72Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6pd1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Trede Trede]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PD1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PD1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6pd1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Treponema_denticola_ATCC_35405 Treponema denticola ATCC 35405]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PD1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.72Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TDE_1415 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243275 TREDE])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6pd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pd1 OCA], [http://pdbe.org/6pd1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pd1 RCSB], [http://www.ebi.ac.uk/pdbsum/6pd1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pd1 ProSAT]</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=6pd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pd1 OCA], [https://pdbe.org/6pd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pd1 RCSB], [https://www.ebi.ac.uk/pdbsum/6pd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pd1 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PNTCW_TREDE PNTCW_TREDE] Bifunctional transferase involved in the biosynthesis of cell-surface phosphonates (PubMed:31420548). The aminotransferase region catalyzes the transformation of phosphonoacetaldehyde (PnAA) to 2-aminoethylphosphonate (AEP) (PubMed:31420548). The cytidylyltransferase region catalyzes the activation of 2-aminoethylphosphonate (AEP) to CMP-2-aminoethylphosphonate (CMP-AEP) (PubMed:31420548). Cannot use phosphocholine (PubMed:31420548). Exhibits strong activity towards CTP, limited activity towards ATP and no activity with GTP (PubMed:31420548).<ref>PMID:31420548</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Trede]] | + | [[Category: Treponema denticola ATCC 35405]] |
| - | [[Category: Suits, M D.L]] | + | [[Category: Suits MDL]] |
| - | [[Category: Whiteside, J]] | + | [[Category: Whiteside J]] |
| - | [[Category: Biosynthetic protein]]
| + | |
| - | [[Category: Cytidylyltransferase]]
| + | |
| - | [[Category: Phosphonate]]
| + | |
| Structural highlights
6pd1 is a 4 chain structure with sequence from Treponema denticola ATCC 35405. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.72Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PNTCW_TREDE Bifunctional transferase involved in the biosynthesis of cell-surface phosphonates (PubMed:31420548). The aminotransferase region catalyzes the transformation of phosphonoacetaldehyde (PnAA) to 2-aminoethylphosphonate (AEP) (PubMed:31420548). The cytidylyltransferase region catalyzes the activation of 2-aminoethylphosphonate (AEP) to CMP-2-aminoethylphosphonate (CMP-AEP) (PubMed:31420548). Cannot use phosphocholine (PubMed:31420548). Exhibits strong activity towards CTP, limited activity towards ATP and no activity with GTP (PubMed:31420548).[1]
Publication Abstract from PubMed
Phosphonates are rare and unusually bioactive natural products. However, most bacterial phosphonate biosynthetic capacity is dedicated to tailoring cell surfaces with molecules like 2-aminoethylphosphonate (AEP). Although phosphoenolpyruvate mutase (Ppm)-catalyzed installation of C-P bonds is known, subsequent phosphonyl tailoring (Pnt) pathway steps remain enigmatic. Here we identify nucleotidyltransferases in over two-thirds of phosphonate biosynthetic gene clusters, including direct fusions to ~60% of Ppm enzymes. We characterize two putative phosphonyl tailoring cytidylyltransferases (PntCs) that prefer AEP over phosphocholine (P-Cho) - a similar substrate used by the related enzyme LicC, which is a virulence factor in Streptococcus pneumoniae. PntC structural analyses reveal steric discrimination against phosphocholine. These findings highlight nucleotidyl activation as a predominant chemical logic in phosphonate biosynthesis and set the stage for probing diverse phosphonyl tailoring pathways.
The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis.,Rice K, Batul K, Whiteside J, Kelso J, Papinski M, Schmidt E, Pratasouskaya A, Wang D, Sullivan R, Bartlett C, Weadge JT, Van der Kamp MW, Moreno-Hagelsieb G, Suits MD, Horsman GP Nat Commun. 2019 Aug 16;10(1):3698. doi: 10.1038/s41467-019-11627-6. PMID:31420548[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Rice K, Batul K, Whiteside J, Kelso J, Papinski M, Schmidt E, Pratasouskaya A, Wang D, Sullivan R, Bartlett C, Weadge JT, Van der Kamp MW, Moreno-Hagelsieb G, Suits MD, Horsman GP. The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. Nat Commun. 2019 Aug 16;10(1):3698. doi: 10.1038/s41467-019-11627-6. PMID:31420548 doi:http://dx.doi.org/10.1038/s41467-019-11627-6
- ↑ Rice K, Batul K, Whiteside J, Kelso J, Papinski M, Schmidt E, Pratasouskaya A, Wang D, Sullivan R, Bartlett C, Weadge JT, Van der Kamp MW, Moreno-Hagelsieb G, Suits MD, Horsman GP. The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis. Nat Commun. 2019 Aug 16;10(1):3698. doi: 10.1038/s41467-019-11627-6. PMID:31420548 doi:http://dx.doi.org/10.1038/s41467-019-11627-6
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