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| - | [[Image:2fpg.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP== |
| - | |PDB= 2fpg |SIZE=350|CAPTION= <scene name='initialview01'>2fpg</scene>, resolution 2.960Å
| + | <StructureSection load='2fpg' size='340' side='right'caption='[[2fpg]], [[Resolution|resolution]] 2.96Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=GDP:GUANOSINE-5'-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene> | + | <table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPG FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.96Å</td></tr> |
| - | |GENE= SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [https://pdbe.org/2fpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [https://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpg ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1euc|1EUC]], [[1eud|1EUD]], [[2fp4|2FP4]], [[2fpi|2FPI]], [[2fpp|2FPP]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/SUCB2_PIG SUCB2_PIG] Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity). |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpg_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </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=2fpg ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP'''
| + | ==See Also== |
| - | | + | *[[Succinyl-CoA synthetase 3D structures|Succinyl-CoA synthetase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | Two isoforms of succinyl-CoA synthetase exist in mammals, one specific for ATP and the other for GTP. The GTP-specific form of pig succinyl-CoA synthetase has been crystallized in the presence of GTP and the structure determined to 2.1 A resolution. GTP is bound in the ATP-grasp domain, where interactions of the guanine base with a glutamine residue (Gln-20beta) and with backbone atoms provide the specificity. The gamma-phosphate interacts with the side chain of an arginine residue (Arg-54beta) and with backbone amide nitrogen atoms, leading to tight interactions between the gamma-phosphate and the protein. This contrasts with the structures of ATP bound to other members of the family of ATP-grasp proteins where the gamma-phosphate is exposed, free to react with the other substrate. To test if GDP would interact with GTP-specific succinyl-CoA synthetase in the same way that ADP interacts with other members of the family of ATP-grasp proteins, the structure of GDP bound to GTP-specific succinyl-CoA synthetase was also determined. A comparison of the conformations of GTP and GDP shows that the bases adopt the same position but that changes in conformation of the ribose moieties and the alpha- and beta-phosphates allow the gamma-phosphate to interact with the arginine residue and amide nitrogen atoms in GTP, while the beta-phosphate interacts with these residues in GDP. The complex of GTP with succinyl-CoA synthetase shows that the enzyme is able to protect GTP from hydrolysis when the active-site histidine residue is not in position to be phosphorylated.
| + | [[Category: Large Structures]] |
| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2FPG is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA].
| + | |
| - | | + | |
| - | ==Reference==
| + | |
| - | Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase., Fraser ME, Hayakawa K, Hume MS, Ryan DG, Brownie ER, J Biol Chem. 2006 Apr 21;281(16):11058-65. Epub 2006 Feb 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16481318 16481318]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Succinate--CoA ligase (GDP-forming)]]
| + | |
| | [[Category: Sus scrofa]] | | [[Category: Sus scrofa]] |
| - | [[Category: Fraser, M E.]] | + | [[Category: Fraser ME]] |
| - | [[Category: active site histidine residue]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:05:58 2008''
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