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| | <StructureSection load='5nof' size='340' side='right'caption='[[5nof]], [[Resolution|resolution]] 2.42Å' scene=''> | | <StructureSection load='5nof' size='340' side='right'caption='[[5nof]], [[Resolution|resolution]] 2.42Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5nof]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NOF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5nof]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NOF FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.42Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Anthranilate_phosphoribosyltransferase Anthranilate phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.18 2.4.2.18] </span></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5nof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nof OCA], [http://pdbe.org/5nof PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nof RCSB], [http://www.ebi.ac.uk/pdbsum/5nof PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nof 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=5nof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nof OCA], [https://pdbe.org/5nof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nof RCSB], [https://www.ebi.ac.uk/pdbsum/5nof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nof ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TRPD_THEKO TRPD_THEKO]] Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). | + | [https://www.uniprot.org/uniprot/TRPD_THEKO TRPD_THEKO] Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA). |
| | <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: Anthranilate phosphoribosyltransferase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Papageorgiou, A C]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Perveen, S]] | + | [[Category: Papageorgiou AC]] |
| - | [[Category: Rashid, N]] | + | [[Category: Perveen S]] |
| - | [[Category: Phosphoribosyltransferase]] | + | [[Category: Rashid N]] |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Tryptophan biosynthesis]]
| + | |
| Structural highlights
Function
TRPD_THEKO Catalyzes the transfer of the phosphoribosyl group of 5-phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA).
Publication Abstract from PubMed
Anthranilate phosphoribosyltransferase (TrpD) is involved in tryptophan biosynthesis, catalyzing the transfer of a phosphoribosyl group to anthranilate, leading to the generation of phosphoribosyl anthranilate. TrpD belongs to the phosphoribosyltransferase (PRT) superfamily and is the only member of the structural class IV. X-ray structures of TrpD from seven species have been solved to date. Here, functional and structural characterization of a recombinant TrpD from hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkTrpD) was carried out. Contrary to previously characterized Mg2+-dependent TrpD enzymes, TkTrpD was found to have a unique divalent cation dependency characterized by maximum activity in the presence of Zn2+ (1580 mumol.min-1.mg-1, the highest reported for any TrpD) followed by Ca2+ (948 mumol.min-1.mg-1) and Mg2+ (711 mumol.min-1.mg-1). TkTrpD displayed an unusually low thermostability compared to other previously characterized proteins from T. kodakarensis KOD1. The crystal structure of TkTrpD was determined in free form and in the presence of Zn2+ to 1.9 and 2.4 A resolutions, respectively. TkTrpD structure displayed the typical PRT fold similar to other class IV PRTs, with a small N-terminal alpha-helical domain and a larger C-terminal alpha/beta domain. Electron densities for Zn2+ were identified at the expected zinc-binding motif, DE(217-218), of the enzyme in each subunit of the dimer. Two additional Zn2+ were found at a new dimer interface formed in the presence of Zn2+. A fifth Zn2+ was found bound to Glu118 at crystal lattice contacts and a sixth one was ligated with Glu235. Based on the TkTrpD-Zn2+ structure, it is suggested that the formation of a new dimer may be responsible for the higher enzyme activity of TkTrpD in the presence of Zn2+ ions.
Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure.,Perveen S, Rashid N, Tang XF, Imanaka T, Papageorgiou AC FEBS Open Bio. 2017 Jul 24;7(8):1217-1230. doi: 10.1002/2211-5463.12264., eCollection 2017 Aug. PMID:28781961[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Perveen S, Rashid N, Tang XF, Imanaka T, Papageorgiou AC. Anthranilate phosphoribosyltransferase from the hyperthermophilic archaeon Thermococcus kodakarensis shows maximum activity with zinc and forms a unique dimeric structure. FEBS Open Bio. 2017 Jul 24;7(8):1217-1230. doi: 10.1002/2211-5463.12264., eCollection 2017 Aug. PMID:28781961 doi:http://dx.doi.org/10.1002/2211-5463.12264
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