2fp4: Difference between revisions

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-[[Image:2fp4.png|left|200px]]
-{{STRUCTURE_2fp4|  PDB=2fp4  |  SCENE=  }}
+==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GTP==
+<StructureSection load='2fp4' size='340' side='right'caption='[[2fp4]], [[Resolution|resolution]] 2.08&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2fp4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. The October 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Citric Acid Cycle''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_10 10.2210/rcsb_pdb/mom_2012_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FP4 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=NEP:N1-PHOSPHONOHISTIDINE'>NEP</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1euc|1euc]], [[1eud|1eud]], [[2fpg|2fpg]], [[2fpi|2fpi]], [[2fpp|2fpp]]</div></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), SUCLG2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate--CoA_ligase_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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=2fp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fp4 OCA], [https://pdbe.org/2fp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fp4 RCSB], [https://www.ebi.ac.uk/pdbsum/2fp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fp4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/SUCA_PIG SUCA_PIG]] Catalyzes the ATP- or GTP-dependent ligation of succinate and CoA to form succinyl-CoA. The nature of the beta subunit determines the nucleotide specificity (By similarity). [[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/2fp4_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=2fp4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GTP===
+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:16481318<ref>PMID:16481318</ref>
-{{ABSTRACT_PUBMED_16481318}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2fp4" style="background-color:#fffaf0;"></div>
-[[2fp4]] is a 2 chain structure with sequence 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=2FP4 OCA].
 ==See Also==
-*[[Succinyl-CoA synthetase|Succinyl-CoA synthetase]]
+*[[Succinyl-CoA synthetase 3D structures|Succinyl-CoA synthetase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016481318</ref><references group="xtra"/>
+__TOC__
-[[Category: Sus scrofa]]
+</StructureSection>
-[[Category: Fraser, M E.]]
+[[Category: Citric Acid Cycle]]
+[[Category: Large Structures]]
+[[Category: Pig]]
+[[Category: RCSB PDB Molecule of the Month]]
+[[Category: Fraser, M E]]
 [[Category: Active site phosphohistidine residue]]
 [[Category: Ligase]]