8yru
From Proteopedia
(Difference between revisions)
| Line 5: | Line 5: | ||
<table><tr><td colspan='2'>[[8yru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haliscomenobacter_hydrossis_DSM_1100 Haliscomenobacter hydrossis DSM 1100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8YRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8YRU FirstGlance]. <br> | <table><tr><td colspan='2'>[[8yru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haliscomenobacter_hydrossis_DSM_1100 Haliscomenobacter hydrossis DSM 1100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8YRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8YRU 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]] 2Å</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]] 2Å</td></tr> | ||
| - | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZXN:[6-methyl-5-oxidanyl-4-[( | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZXN:[6-methyl-5-oxidanyl-4-[(~{E})-(phenylhydrazinylidene)methyl]pyridin-3-yl]methyl+dihydrogen+phosphate'>ZXN</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=8yru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8yru OCA], [https://pdbe.org/8yru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8yru RCSB], [https://www.ebi.ac.uk/pdbsum/8yru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8yru 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=8yru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8yru OCA], [https://pdbe.org/8yru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8yru RCSB], [https://www.ebi.ac.uk/pdbsum/8yru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8yru ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/F4KWH0_HALH1 F4KWH0_HALH1] | [https://www.uniprot.org/uniprot/F4KWH0_HALH1 F4KWH0_HALH1] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pyridoxal-5'-phosphate (PLP)-dependent transaminases are key enzymes of amino acid metabolism in cells and remarkable biocatalysts of stereoselective amination for process chemistry applications. As cofactor-dependent enzymes, transaminases are prone to cofactor leakage. Here we discuss the holoenzyme-apoenzyme interconversion and the kinetics of PLP incorporation into the apo form of a PLP-dependent transaminase from Haliscomenobacter hydrossis. PLP binding to the apoenzyme was slow in buffer, but was accelerated in the presence of substrates. Two crystal structures of the apoenzyme were obtained: the directly obtained apoenzyme (PDB ID: 7P8O) and the one obtained by soaking crystals of the holoenzyme in a phenylhydrazine solution (PDB ID: 8YRU). The mechanism of PLP association with the apoenzyme was proposed on the basis of structural analysis of these apo forms. Three rearrangement steps, including (I) anchoring of the PLP via the phosphate group, (II) displacement of two loops, and (III) Schiff-bonding between the PLP and the epsilon-amino group of the catalytic lysine residue, reconstituted the active holo form of the transaminase from H. hydrossis. The results obtained allowed us to determine in the active site a permanent part and elements that are assembled by PLP, these findings may be useful for transaminase engineering for biocatalysis. | ||
| + | |||
| + | Incorporation of pyridoxal-5'-phosphate into the apoenzyme: A structural study of D-amino acid transaminase from Haliscomenobacter hydrossis.,Bakunova AK, Matyuta IO, Minyaev ME, Boyko KM, Popov VO, Bezsudnova EY Biochim Biophys Acta Proteins Proteom. 2024 Oct 13;1873(1):141056. doi: , 10.1016/j.bbapap.2024.141056. PMID:39406293<ref>PMID:39406293</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 8yru" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine
| |||||||||||
