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| | <StructureSection load='7cqq' size='340' side='right'caption='[[7cqq]], [[Resolution|resolution]] 2.29Å' scene=''> | | <StructureSection load='7cqq' size='340' side='right'caption='[[7cqq]], [[Resolution|resolution]] 2.29Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7cqq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodovulum_sp._12e13 Rhodovulum sp. 12e13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CQQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CQQ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7cqq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodovulum_sp._12E13 Rhodovulum sp. 12E13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CQQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CQQ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSL:(2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC+ACID'>MSL</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]] 2.295Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glnT, DLJ49_05815 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2203891 Rhodovulum sp. 12E13])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSL:(2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC+ACID'>MSL</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glutamate--ammonia_ligase Glutamate--ammonia ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.1.2 6.3.1.2] </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=7cqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cqq OCA], [https://pdbe.org/7cqq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cqq RCSB], [https://www.ebi.ac.uk/pdbsum/7cqq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cqq 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=7cqq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cqq OCA], [https://pdbe.org/7cqq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cqq RCSB], [https://www.ebi.ac.uk/pdbsum/7cqq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cqq ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/A0A369R1N0_9RHOB A0A369R1N0_9RHOB]] Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.[ARBA:ARBA00003117]
| + | [https://www.uniprot.org/uniprot/A0A369R1N0_9RHOB A0A369R1N0_9RHOB] Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.[ARBA:ARBA00003117] |
| | <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: Glutamate--ammonia ligase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Rhodovulum sp. 12e13]] | + | [[Category: Rhodovulum sp. 12E13]] |
| - | [[Category: Li, C Y]] | + | [[Category: Li CY]] |
| - | [[Category: Zhang, Y Z]] | + | [[Category: Zhang YZ]] |
| - | [[Category: Biosynthetic protein]]
| + | |
| - | [[Category: Gma synthetase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| Structural highlights
Function
A0A369R1N0_9RHOB Catalyzes the ATP-dependent biosynthesis of glutamine from glutamate and ammonia.[ARBA:ARBA00003117]
Publication Abstract from PubMed
Monomethylamine (MMA) is an important climate-active oceanic trace gas and ubiquitous in the oceans. gamma-Glutamylmethylamide synthetase (GmaS) catalyzes the conversion of MMA to gamma-glutamylmethylamide, the first step in MMA metabolism in many marine bacteria. The gmaS gene occurs in approximately 23% of microbial genomes in the surface ocean and is a validated biomarker to detect MMA-utilizing bacteria. However, the catalytic mechanism of GmaS has not been studied because of the lack of structural information. Here, the GmaS from Rhodovulum sp. 12E13 (RhGmaS) was characterized, and the crystal structures of apo-RhGmaS and RhGmaS with different ligands in five states were solved. Based on structural and biochemical analyses, the catalytic mechanism of RhGmaS was explained. ATP is first bound in RhGmaS, leading to a conformational change of a flexible loop (Lys287-Ile305), which is essential for the subsequent binding of glutamate. During the catalysis of RhGmaS, the residue Arg312 participates in polarizing the gamma-phosphate of ATP and in stabilizing the gamma-glutamyl phosphate intermediate; Asp177 is responsible for the deprotonation of MMA, assisting the attack of MMA on gamma-glutamyl phosphate to produce a tetrahedral intermediate; and Glu186 acts as a catalytic base to abstract a proton from the tetrahedral intermediate to finally generate glutamylmethylamide. Sequence analysis suggested that the catalytic mechanism of RhGmaS proposed in this study has universal significance in bacteria containing GmaS. Our results provide novel insights into MMA metabolism, contributing to a better understanding of MMA catabolism in global carbon and nitrogen cycles.
Crystal structures of gamma-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine.,Wang N, Chen XL, Gao C, Peng M, Wang P, Zhang N, Li F, Yang GP, Shen QT, Li S, Chen Y, Zhang YZ, Li CY J Biol Chem. 2021 Jan-Jun;296:100081. doi: 10.1074/jbc.RA120.015952. Epub 2020, Nov 21. PMID:33199371[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wang N, Chen XL, Gao C, Peng M, Wang P, Zhang N, Li F, Yang GP, Shen QT, Li S, Chen Y, Zhang YZ, Li CY. Crystal structures of gamma-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine. J Biol Chem. 2021 Jan-Jun;296:100081. doi: 10.1074/jbc.RA120.015952. Epub 2020, Nov 21. PMID:33199371 doi:http://dx.doi.org/10.1074/jbc.RA120.015952
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