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| - | {{Large structure}}
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| | ==Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with N-(dihydroxymethyl)putrescine== | | ==Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with N-(dihydroxymethyl)putrescine== |
| - | <StructureSection load='5h8i' size='340' side='right' caption='[[5h8i]], [[Resolution|resolution]] 1.97Å' scene=''> | + | <StructureSection load='5h8i' size='340' side='right'caption='[[5h8i]], [[Resolution|resolution]] 1.97Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5h8i]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Barrel_medic Barrel medic]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H8I FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5h8i]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Medicago_truncatula Medicago truncatula]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H8I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H8I 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=N2H:(4-AZANYLBUTYLAMINO)METHANEDIOL'>N2H</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 1.97Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h8j|5h8j]], [[5h8k|5h8k]], [[5h8l|5h8l]]</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=N2H:(4-AZANYLBUTYLAMINO)METHANEDIOL'>N2H</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MTR_2g086600 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3880 Barrel medic])</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=5h8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8i OCA], [https://pdbe.org/5h8i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h8i RCSB], [https://www.ebi.ac.uk/pdbsum/5h8i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8i 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/N-carbamoylputrescine_amidase N-carbamoylputrescine amidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.53 3.5.1.53] </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=5h8i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h8i OCA], [http://pdbe.org/5h8i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h8i RCSB], [http://www.ebi.ac.uk/pdbsum/5h8i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h8i ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | {{Large structure}}
| + | == Function == |
| | + | [https://www.uniprot.org/uniprot/G7ITU5_MEDTR G7ITU5_MEDTR] |
| | <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: Barrel medic]] | + | [[Category: Large Structures]] |
| - | [[Category: N-carbamoylputrescine amidase]] | + | [[Category: Medicago truncatula]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Dauter Z]] |
| - | [[Category: Malinska, M]] | + | [[Category: Malinska M]] |
| - | [[Category: Ruszkowski, M]] | + | [[Category: Ruszkowski M]] |
| - | [[Category: Sekula, B]] | + | [[Category: Sekula B]] |
| - | [[Category: Alpha-beta-beta-alpha sandwich fold]]
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| - | [[Category: Amidase]]
| + | |
| - | [[Category: Helical octamer]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Intermediate]]
| + | |
| Structural highlights
5h8i is a 16 chain structure with sequence from Medicago truncatula. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.97Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
G7ITU5_MEDTR
Publication Abstract from PubMed
Putrescine, 1,4-diaminobutane, is an intermediate in the biosynthesis of more complexed polyamines, spermidine and spermine. Unlike other eukaryotes, plants have evolved a multistep pathway for putrescine biosynthesis that utilizes arginine. In the final reaction, N-carbamoylputrescine is hydrolyzed to putrescine by N-carbamoylputrescine amidohydrolase (CPA, EC 3.5.1.53). During the hydrolysis, consecutive nucleophilic attacks on the substrate by Cys158 and water lead to formation of putrescine and two by-products, ammonia and carbon dioxide. CPA from the model legume plant, Medicago truncatula (MtCPA), was investigated in this work. Four crystal structures were determined: the wild-type MtCPA in complex with the reaction intermediate, N-(dihydroxymethyl)putrescine as well as with cadaverine, which is a longer analog of putrescine; and also structures of MtCPA-C158S mutant unliganded and with putrescine. MtCPA assembles into octamers, which resemble an incomplete left-handed helical twist. The active site of MtCPA is funnel-like shaped, and its entrance is walled with a contribution of the neighboring protein subunits. Deep inside the catalytic cavity, Glu48, Lys121, and Cys158 form the catalytic triad. In this studies, we have highlighted the key residues, highly conserved among the plant kingdom, responsible for the activity and selectivity of MtCPA toward N-carbamoylputrescine. Moreover, since, according to previous reports, a close MtCPA relative from Arabidopsis thaliana, along with several other nitrilase-like proteins, are subjected to allosteric regulation by substrates, we have used the structural information to indicate a putative secondary binding site. Based on the docking experiment, we postulate that this site is adjacent to the entrance to the catalytic pocket.
Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants.,Sekula B, Ruszkowski M, Malinska M, Dauter Z Front Plant Sci. 2016 Mar 30;7:350. doi: 10.3389/fpls.2016.00350. eCollection, 2016. PMID:27066023[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sekula B, Ruszkowski M, Malinska M, Dauter Z. Structural Investigations of N-carbamoylputrescine Amidohydrolase from Medicago truncatula: Insights into the Ultimate Step of Putrescine Biosynthesis in Plants. Front Plant Sci. 2016 Mar 30;7:350. doi: 10.3389/fpls.2016.00350. eCollection, 2016. PMID:27066023 doi:http://dx.doi.org/10.3389/fpls.2016.00350
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