|
|
| (11 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:1gso.gif|left|200px]] | |
| | | | |
| - | <!--
| + | ==GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI.== |
| - | The line below this paragraph, containing "STRUCTURE_1gso", creates the "Structure Box" on the page.
| + | <StructureSection load='1gso' size='340' side='right'caption='[[1gso]], [[Resolution|resolution]] 1.60Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1gso]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GSO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GSO FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</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=1gso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gso OCA], [https://pdbe.org/1gso PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gso RCSB], [https://www.ebi.ac.uk/pdbsum/1gso PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gso ProSAT]</span></td></tr> |
| - | {{STRUCTURE_1gso| PDB=1gso | SCENE= }}
| + | </table> |
| - | | + | == Function == |
| - | '''GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI.'''
| + | [https://www.uniprot.org/uniprot/PUR2_ECOLI PUR2_ECOLI] |
| - | | + | == Evolutionary Conservation == |
| - | | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | ==Overview== | + | Check<jmol> |
| - | Glycinamide ribonucleotide synthetase (GAR-syn) catalyzes the second step of the de novo purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine, and ATP to glycinamide ribonucleotide (GAR), ADP, and Pi. GAR-syn containing an N-terminal polyhistidine tag was expressed as the SeMet incorporated protein for crystallographic studies. In addition, the protein as isolated contains a Pro294Leu mutation. This protein was crystallized, and the structure solved using multiple-wavelength anomalous diffraction (MAD) phase determination and refined to 1.6 A resolution. GAR-syn adopts an alpha/beta structure that consists of four domains labeled N, A, B, and C. The N, A, and C domains are clustered to form a large central core structure whereas the smaller B domain is extended outward. Two hinge regions, which might readily facilitate interdomain movement, connect the B domain and the main core. A search of structural databases showed that the structure of GAR-syn is similar to D-alanine:D-alanine ligase, biotin carboxylase, and glutathione synthetase, despite low sequence similarity. These four enzymes all utilize similar ATP-dependent catalytic mechanisms even though they catalyze different chemical reactions. Another ATP-binding enzyme with low sequence similarity but unknown function, synapsin Ia, was also found to share high structural similarity with GAR-syn. Interestingly, the GAR-syn N domain shows similarity to the N-terminal region of glycinamide ribonucleotide transformylase and several dinucleotide-dependent dehydrogenases. Models of ADP and GAR binding were generated based on structure and sequence homology. On the basis of these models, the active site lies in a cleft between the large domain and the extended B domain. Most of the residues that facilitate ATP binding belong to the A or B domains. The N and C domains appear to be largely responsible for substrate specificity. The structure of GAR-syn allows modeling studies of possible channeling complexes with PPRP amidotransferase.
| + | <jmolCheckbox> |
| - | | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gs/1gso_consurf.spt"</scriptWhenChecked> |
| - | ==About this Structure== | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | 1GSO is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GSO OCA].
| + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | | + | </jmolCheckbox> |
| - | ==Reference== | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gso ConSurf]. |
| - | X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli., Wang W, Kappock TJ, Stubbe J, Ealick SE, Biochemistry. 1998 Nov 10;37(45):15647-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9843369 9843369] | + | <div style="clear:both"></div> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Phosphoribosylamine--glycine ligase]] | + | [[Category: Large Structures]] |
| - | [[Category: Single protein]]
| + | [[Category: Ealick SE]] |
| - | [[Category: Ealick, S E.]] | + | [[Category: Kappock TJ]] |
| - | [[Category: Kappock, T J.]] | + | [[Category: Stubbe J]] |
| - | [[Category: Stubbe, J.]] | + | [[Category: Wang W]] |
| - | [[Category: Wang, W.]] | + | |
| - | [[Category: Atp-grasp]]
| + | |
| - | [[Category: Gar-syn]]
| + | |
| - | [[Category: Glycinamide ribonucleotide synthetase]]
| + | |
| - | [[Category: Purine de novo biosynthetic pathway]]
| + | |
| - | [[Category: Substrate channeling]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:57:40 2008''
| + | |
