|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6vl7' size='340' side='right'caption='[[6vl7]], [[Resolution|resolution]] 2.14Å' scene=''> | | <StructureSection load='6vl7' size='340' side='right'caption='[[6vl7]], [[Resolution|resolution]] 2.14Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6vl7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudoalteromonas_luteoviolacea_dsm_6061 Pseudoalteromonas luteoviolacea dsm 6061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VL7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VL7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6vl7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudoalteromonas_luteoviolacea_DSM_6061 Pseudoalteromonas luteoviolacea DSM 6061]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VL7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VL7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.14Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6byw|6byw]], [[6eer|6eer]]</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=6vl7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vl7 OCA], [https://pdbe.org/6vl7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vl7 RCSB], [https://www.ebi.ac.uk/pdbsum/6vl7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vl7 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">N475_19905 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1365250 Pseudoalteromonas luteoviolacea DSM 6061])</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=6vl7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vl7 OCA], [http://pdbe.org/6vl7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vl7 RCSB], [http://www.ebi.ac.uk/pdbsum/6vl7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vl7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A161XU12_9GAMM A0A161XU12_9GAMM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 24: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pseudoalteromonas luteoviolacea dsm 6061]] | + | [[Category: Pseudoalteromonas luteoviolacea DSM 6061]] |
| - | [[Category: Yukl, E T]] | + | [[Category: Yukl ET]] |
| - | [[Category: Ctq]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| Structural highlights
6vl7 is a 4 chain structure with sequence from Pseudoalteromonas luteoviolacea DSM 6061. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.14Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A161XU12_9GAMM
Publication Abstract from PubMed
The quinoprotein glycine oxidase from the marine bacterium Pseudoalteromonas luteoviolacea (PlGoxA) uses a protein-derived cysteine tryptophylquinone (CTQ) cofactor to catalyze conversion of glycine to glyoxylate and ammonia. This homotetremeric enzyme exhibits strong cooperativity towards glycine binding. It is a good model for studying enzyme kinetics and cooperativity, specifically for being able to separate those aspects of protein function through directed mutagenesis. Variant proteins were generated with mutations in four active-site residues, Phe-316, His-583, Tyr-766 and His-767. Structures for glycine-soaked crystals were obtained for each. Different mutations had differential effects on kcat and K0.5 for catalysis, K0.5 for substrate binding, and the Hill coefficients describing the steady-state kinetics or substrate binding. Phe-316 and Tyr-766 variants retained catalytic activity, albeit with altered kinetics and cooperativity. Substitutions of His-583 revealed that it is essential for glycine binding and the structure of H583C PlGoxA had no active-site glycine present in glycine-soaked crystals. The structure of H767A PlGoxA revealed a previously undetected reaction intermediate, a carbinolamine product-reduced CTQ adduct, and exhibited only negligible activity. The results of these experiments, as well as those with the native enzyme and previous variants enabled construction of a detailed mechanism for the reductive half-reaction of glycine oxidation. This proposed mechanism includes three discrete reaction intermediates that are covalently bound to CTQ during the reaction, two of which have now been structurally characterized by X-ray crystallography.
Roles of active site residues in catalysis, substrate binding, cooperativity and the reaction mechanism of the quinoprotein glycine oxidase.,Mamounis KJ, Yukl ET, Davidson VL J Biol Chem. 2020 Mar 31. pii: RA120.013198. doi: 10.1074/jbc.RA120.013198. PMID:32234764[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Mamounis KJ, Yukl ET, Davidson VL. Roles of active site residues in catalysis, substrate binding, cooperativity and the reaction mechanism of the quinoprotein glycine oxidase. J Biol Chem. 2020 Mar 31. pii: RA120.013198. doi: 10.1074/jbc.RA120.013198. PMID:32234764 doi:http://dx.doi.org/10.1074/jbc.RA120.013198
|
