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| | ==Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine== | | ==Crystal structure of putrescine transcarbamylase from Enterococcus faecalis with N-(phosphonoacetyl)-putrescine== |
| - | <StructureSection load='4a8h' size='340' side='right' caption='[[4a8h]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='4a8h' size='340' side='right'caption='[[4a8h]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4a8h]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterococcus_proteiformis"_thiercelin_and_jouhaud_1903 "enterococcus proteiformis" thiercelin and jouhaud 1903]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4A8H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4a8h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterococcus_faecalis Enterococcus faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A8H 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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PUW:N-(PHOSPHONOACETYL)-PUTRESCINE'>PUW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4a8t|4a8t]], [[4a8p|4a8p]]</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=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=PUW:N-(PHOSPHONOACETYL)-PUTRESCINE'>PUW</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Putrescine_carbamoyltransferase Putrescine carbamoyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.3.6 2.1.3.6] </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=4a8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a8h OCA], [https://pdbe.org/4a8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a8h RCSB], [https://www.ebi.ac.uk/pdbsum/4a8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a8h 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=4a8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a8h OCA], [http://pdbe.org/4a8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4a8h RCSB], [http://www.ebi.ac.uk/pdbsum/4a8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4a8h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PTC_ENTFA PTC_ENTFA]] Catalyzes the phosphorolysis of N-carbamoylputrescine to form carbamoyl phosphate and putrescine. Is involved in the degradation pathway of the polyamine agmatine. Also has weak activity with ornithine and cadaverine.<ref>PMID:4621632</ref> | + | [https://www.uniprot.org/uniprot/PTC_ENTFA PTC_ENTFA] Catalyzes the phosphorolysis of N-carbamoylputrescine to form carbamoyl phosphate and putrescine. Is involved in the degradation pathway of the polyamine agmatine. Also has weak activity with ornithine and cadaverine.<ref>PMID:4621632</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Enterococcus proteiformis thiercelin and jouhaud 1903]] | + | [[Category: Enterococcus faecalis]] |
| - | [[Category: Putrescine carbamoyltransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Gil-Ortiz, F]] | + | [[Category: Gil-Ortiz F]] |
| - | [[Category: Polo, L M]] | + | [[Category: Polo LM]] |
| - | [[Category: Rubio, V]] | + | [[Category: Rubio V]] |
| - | [[Category: Agmatine deiminase route]]
| + | |
| - | [[Category: Ornithine]]
| + | |
| - | [[Category: Ornithine arginine deiminase]]
| + | |
| - | [[Category: Palo]]
| + | |
| - | [[Category: Papu]]
| + | |
| - | [[Category: Phosphonoacetylputrescine]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
4a8h is a 2 chain structure with sequence from Enterococcus faecalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.5Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
PTC_ENTFA Catalyzes the phosphorolysis of N-carbamoylputrescine to form carbamoyl phosphate and putrescine. Is involved in the degradation pathway of the polyamine agmatine. Also has weak activity with ornithine and cadaverine.[1]
Publication Abstract from PubMed
Transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (CP) to an amine. Although aspartate transcarbamylase and ornithine transcarbamylase (OTC) are well characterized, little was known about putrescine transcarbamylase (PTC), the enzyme that generates CP for ATP production in the fermentative catabolism of agmatine. We demonstrate that PTC (from Enterococcus faecalis), in addition to using putrescine, can utilize L-ornithine as a poor substrate. Crystal structures at 2.5 A and 2.0 A resolutions of PTC bound to its respective bisubstrate analog inhibitors for putrescine and ornithine use, N-(phosphonoacetyl)-putrescine and delta-N-(phosphonoacetyl)-L-ornithine, shed light on PTC preference for putrescine. Except for a highly prominent C-terminal helix that projects away and embraces an adjacent subunit, PTC closely resembles OTCs, suggesting recent divergence of the two enzymes. Since differences between the respective 230 and SMG loops of PTC and OTC appeared to account for the differential preference of these enzymes for putrescine and ornithine, we engineered the 230-loop of PTC to make it to resemble the SMG loop of OTCs, increasing the activity with ornithine and greatly decreasing the activity with putrescine. We also examined the role of the C-terminal helix that appears a constant and exclusive PTC trait. The enzyme lacking this helix remained active but the PTC trimer stability appeared decreased, since some of the enzyme eluted as monomers from a gel filtration column. In addition, truncated PTC tended to aggregate to hexamers, as shown both chromatographically and by X-ray crystallography. Therefore, the extra C-terminal helix plays a dual role: it stabilizes the PTC trimer and, by shielding helix 1 of an adjacent subunit, it prevents the supratrimeric oligomerizations of obscure significance observed with some OTCs. Guided by the structural data we identify signature traits that permit easy and unambiguous annotation of PTC sequences.
New insight into the transcarbamylase family: the structure of putrescine transcarbamylase, a key catalyst for fermentative utilization of agmatine.,Polo LM, Gil-Ortiz F, Cantin A, Rubio V PLoS One. 2012;7(2):e31528. Epub 2012 Feb 20. PMID:22363663[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Roon RJ, Barker HA. Fermentation of agmatine in Streptococcus faecalis: occurrence of putrescine transcarbamoylase. J Bacteriol. 1972 Jan;109(1):44-50. PMID:4621632
- ↑ Polo LM, Gil-Ortiz F, Cantin A, Rubio V. New insight into the transcarbamylase family: the structure of putrescine transcarbamylase, a key catalyst for fermentative utilization of agmatine. PLoS One. 2012;7(2):e31528. Epub 2012 Feb 20. PMID:22363663 doi:10.1371/journal.pone.0031528
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