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| | ==Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8== | | ==Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8== |
| - | <StructureSection load='2ip4' size='340' side='right' caption='[[2ip4]], [[Resolution|resolution]] 2.80Å' scene=''> | + | <StructureSection load='2ip4' size='340' side='right'caption='[[2ip4]], [[Resolution|resolution]] 2.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ip4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IP4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ip4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IP4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.8Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0811 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=2ip4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip4 OCA], [https://pdbe.org/2ip4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ip4 RCSB], [https://www.ebi.ac.uk/pdbsum/2ip4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ip4 ProSAT], [https://www.topsan.org/Proteins/RSGI/2ip4 TOPSAN]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ip4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip4 OCA], [http://pdbe.org/2ip4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ip4 RCSB], [http://www.ebi.ac.uk/pdbsum/2ip4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ip4 ProSAT], [http://www.topsan.org/Proteins/RSGI/2ip4 TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q5SK40_THET8 Q5SK40_THET8] |
| | == 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: Phosphoribosylamine--glycine ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Thet8]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Baba, S]] | + | [[Category: Baba S]] |
| - | [[Category: Ebihara, A]] | + | [[Category: Ebihara A]] |
| - | [[Category: Fukai, Y]] | + | [[Category: Fukai Y]] |
| - | [[Category: Ishii, T]] | + | [[Category: Ishii T]] |
| - | [[Category: Kanagawa, M]] | + | [[Category: Kanagawa M]] |
| - | [[Category: Kawai, G]] | + | [[Category: Kawai G]] |
| - | [[Category: Kawai, H]] | + | [[Category: Kawai H]] |
| - | [[Category: Nakagawa, N]] | + | [[Category: Nakagawa N]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Sampei G]] |
| - | [[Category: Sampei, G]] | + | [[Category: Yanai H]] |
| - | [[Category: Yanai, H]] | + | |
| - | [[Category: Gar synthetase]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Purd]]
| + | |
| - | [[Category: Purine nucleotide]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Thermus thermophilus]]
| + | |
| Structural highlights
Function
Q5SK40_THET8
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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