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| | ==Crystal structure of GAR synthetase from Geobacillus kaustophilus== | | ==Crystal structure of GAR synthetase from Geobacillus kaustophilus== |
| - | <StructureSection load='2yrw' size='340' side='right' caption='[[2yrw]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='2yrw' size='340' side='right'caption='[[2yrw]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2yrw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2yrw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_kaustophilus Geobacillus kaustophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YRW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gso|1gso]], [[2yrx|2yrx]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylamine--glycine_ligase Phosphoribosylamine--glycine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.13 6.3.4.13] </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=2yrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrw OCA], [https://pdbe.org/2yrw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yrw RCSB], [https://www.ebi.ac.uk/pdbsum/2yrw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrw ProSAT], [https://www.topsan.org/Proteins/RSGI/2yrw TOPSAN]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrw OCA], [http://pdbe.org/2yrw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yrw RCSB], [http://www.ebi.ac.uk/pdbsum/2yrw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrw ProSAT], [http://www.topsan.org/Proteins/RSGI/2yrw TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5L3C7_GEOKA Q5L3C7_GEOKA] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus kaustophilus prickett 1928]] | + | [[Category: Geobacillus kaustophilus]] |
| - | [[Category: Phosphoribosylamine--glycine ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Baba, S]] | + | [[Category: Baba S]] |
| - | [[Category: Kanagawa, M]] | + | [[Category: Kanagawa M]] |
| - | [[Category: Kawai, G]] | + | [[Category: Kawai G]] |
| - | [[Category: Kuramitsu, S]] | + | [[Category: Kuramitsu S]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Sampei G]] |
| - | [[Category: Sampei, G]] | + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Atp binding]]
| + | |
| - | [[Category: Gar synthetase]]
| + | |
| - | [[Category: Glycinamide ribonucleotide synthetase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Purine nucleotide biosynthetic pathway]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| Structural highlights
Function
Q5L3C7_GEOKA
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Glycinamide ribonucleotide synthetase (GAR-syn, PurD) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and ATP to glycinamide ribonucleotide (GAR), ADP and Pi. In the present study, crystal structures of GAR-syn's from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus were determined in apo forms. Crystal structures in ligand-bound forms were also determined for G. kaustophilus and A. aeolicus proteins. In general, overall structures of GAR-syn's are similar to each other. However, the orientations of the B domains are varied among GAR-syn's and the MD simulation suggested the mobility of the B domain. Furthermore, it was demonstrated that the B loop in the B domain fixes the position of the beta- and gamma- phosphate groups of the bound ATP. The structures of GAR-syn's and the bound ligands were compared with each other in detail, and structures of GAR-syn's with full ligands, as well as the possible reaction mechanism, were proposed.
Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria.,Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G J Biochem. 2010 Oct;148(4):429-38. Epub 2010 Aug 16. PMID:20716513[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G. Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria. J Biochem. 2010 Oct;148(4):429-38. Epub 2010 Aug 16. PMID:20716513 doi:10.1093/jb/mvq088
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