7vnt: Difference between revisions
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==Structure of aminotransferase-substrate complex== | |||
<StructureSection load='7vnt' size='340' side='right'caption='[[7vnt]], [[Resolution|resolution]] 1.92Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7vnt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNT FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.92Å</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=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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=7vnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnt OCA], [https://pdbe.org/7vnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnt RCSB], [https://www.ebi.ac.uk/pdbsum/7vnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnt ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/O50131_PYRHO O50131_PYRHO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Ornithine delta-aminotransferase (Orn-AT) activity was detected for the enzyme annotated as a gamma-aminobutyrate aminotransferase encoded by PH1423 gene from Pyrococcus horikoshii OT-3. Crystal structures of this novel archaeal omega-aminotransferase were determined for the enzyme in complex with pyridoxal 5'-phosphate (PLP), in complex with PLP and l-ornithine (l-Orn), and in complex with N-(5'-phosphopyridoxyl)-l-glutamate (PLP-l-Glu). Although the sequence identity was relatively low (28%), the main-chain coordinates of P. horikoshii Orn-AT monomer showed notable similarity to those of human Orn-AT. However, the residues recognizing the alpha-amino group of l-Orn differ between the two enzymes. In human Orn-AT, Tyr55 and Tyr85 recognize the alpha-amino group, whereas the side chains of Thr92* and Asp93*, which arise from a loop in the neighboring subunit, form hydrogen bonds with the alpha-amino group of the substrate in P. horikoshii enzyme. Site-directed mutagenesis suggested that Asp93* plays critical roles in maintaining high affinity for the substrate. This study provides new insight into the substrate binding of a novel type of Orn-AT. Moreover, the structure of the enzyme with the reaction-intermediate analogue PLP-l-Glu bound provides the first structural evidence for the "Glu switch" mechanism in the dual substrate specificity of Orn-AT. | |||
Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.,Kawakami R, Ohshida T, Hayashi J, Yoneda K, Furumoto T, Ohshima T, Sakuraba H Int J Biol Macromol. 2022 May 31;208:731-740. doi:, 10.1016/j.ijbiomac.2022.03.114. Epub 2022 Mar 23. PMID:35337912<ref>PMID:35337912</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7vnt" style="background-color:#fffaf0;"></div> | ||
[[Category: Ohshida | == References == | ||
[[Category: Ohshima | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus horikoshii OT3]] | |||
[[Category: Ohshida T]] | |||
[[Category: Ohshima T]] | |||
[[Category: Sakuraba H]] | |||
Latest revision as of 20:28, 29 November 2023
Structure of aminotransferase-substrate complexStructure of aminotransferase-substrate complex
Structural highlights
FunctionPublication Abstract from PubMedOrnithine delta-aminotransferase (Orn-AT) activity was detected for the enzyme annotated as a gamma-aminobutyrate aminotransferase encoded by PH1423 gene from Pyrococcus horikoshii OT-3. Crystal structures of this novel archaeal omega-aminotransferase were determined for the enzyme in complex with pyridoxal 5'-phosphate (PLP), in complex with PLP and l-ornithine (l-Orn), and in complex with N-(5'-phosphopyridoxyl)-l-glutamate (PLP-l-Glu). Although the sequence identity was relatively low (28%), the main-chain coordinates of P. horikoshii Orn-AT monomer showed notable similarity to those of human Orn-AT. However, the residues recognizing the alpha-amino group of l-Orn differ between the two enzymes. In human Orn-AT, Tyr55 and Tyr85 recognize the alpha-amino group, whereas the side chains of Thr92* and Asp93*, which arise from a loop in the neighboring subunit, form hydrogen bonds with the alpha-amino group of the substrate in P. horikoshii enzyme. Site-directed mutagenesis suggested that Asp93* plays critical roles in maintaining high affinity for the substrate. This study provides new insight into the substrate binding of a novel type of Orn-AT. Moreover, the structure of the enzyme with the reaction-intermediate analogue PLP-l-Glu bound provides the first structural evidence for the "Glu switch" mechanism in the dual substrate specificity of Orn-AT. Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.,Kawakami R, Ohshida T, Hayashi J, Yoneda K, Furumoto T, Ohshima T, Sakuraba H Int J Biol Macromol. 2022 May 31;208:731-740. doi:, 10.1016/j.ijbiomac.2022.03.114. Epub 2022 Mar 23. PMID:35337912[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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