2fpg: Difference between revisions

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New page: left|200px<br /><applet load="2fpg" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fpg, resolution 2.960Å" /> '''Crystal structure o...
 
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[[Image:2fpg.gif|left|200px]]<br /><applet load="2fpg" size="450" color="white" frame="true" align="right" spinBox="true"
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'''Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP'''<br />


==Overview==
==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP==
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.
<StructureSection load='2fpg' size='340' side='right'caption='[[2fpg]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
== Structural highlights ==
<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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.96&#8491;</td></tr>
<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>
<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>
</table>
== 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>


==About this Structure==
==See Also==
2FPG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with K, PO4 and GDP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA].
*[[Succinyl-CoA synthetase 3D structures|Succinyl-CoA synthetase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=16481318 16481318]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Succinate--CoA ligase (GDP-forming)]]
[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
[[Category: Fraser, M.E.]]
[[Category: Fraser ME]]
[[Category: GDP]]
[[Category: K]]
[[Category: PO4]]
[[Category: active site histidine residue]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:40:50 2007''

Latest revision as of 12:24, 14 February 2024

Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDPCrystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP

Structural highlights

2fpg is a 2 chain structure with sequence from Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.96Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SUCB2_PIG Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2fpg, resolution 2.96Å

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