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1kf0

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(New page: 200px<br /><applet load="1kf0" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kf0, resolution 2.50&Aring;" /> '''Crystal Structure of...)
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[[Image:1kf0.jpg|left|200px]]<br /><applet load="1kf0" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1kf0, resolution 2.50&Aring;" />
 
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'''Crystal Structure of Pig Muscle Phosphoglycerate Kinase Ternary Complex with AMP-PCP and 3PG'''<br />
 
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==Overview==
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==Crystal Structure of Pig Muscle Phosphoglycerate Kinase Ternary Complex with AMP-PCP and 3PG==
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Crystal structure of the ternary complex of pig muscle phosphoglycerate, kinase (PGK) with the substrate 3-phosphoglycerate (3-PG) and the Mg(2+), complex of beta,gamma-methylene-adenosine-5'-triphosphate (AMP-PCP), a, nonreactive analogue of the nucleotide substrate, MgATP, has been, determined by X-ray diffraction at 2.5 A resolution. The overall structure, of the protein exhibits an open conformation, similar to that of the, previously determined ternary complex of the pig muscle enzyme with, beta,gamma-imido-adenosine-5'-triphosphate (AMP-PNP) in place of AMP-PCP, (May, Vas, Harlos, and Blake (1996) Proteins 24, 292-303). The orientation, and details of interactions of the nucleotide phosphates, however, show, marked differences. The beta-phosphate is linked to the conserved Asp 218, i.e., to the N-terminus of helix 8, through the Mg(2+) ion; the previously, observed interactions of the metal complex of AMP-PNP or ADP with the, conserved Asn 336 and the N-terminus of helix 13 are completely absent., These structural differences are maintained themselves in solution, studies. Inhibition and binding experiments show a slightly weaker, interaction of PGK with MgAMP-PCP than with MgAMP-PNP: at pH 7.5, the K(d), values are 1.07 +/- 0.18 and 0.41 +/- 0.08 mM, respectively. The, difference is further enhanced by 3-PG: the K(d) values are 2.80 +/- 0.66, and 0.68 +/- 0.11 mM, respectively. Thus, the previously observed, weakening effect of 3-PG on nucleotide binding (Merli, Szilagyi, Flachner, Rossi, and Vas (2002) Biochemistry 41, 111-119) is more pronounced with, MgAMP-PCP. The discordance between substrate analogues also shows up in, thiol reactivity studies. In their binary complexes, both ATP analogues, protect the fast-reacting thiols of PGK in helix 13 against modification, to similar extent. In their ternary complexes, however, which also contain, bound 3-PG, the protective effect of MgAMP-PCP, but not of MgAMP-PNP, is, largely abolished. This indicates a much smaller effect of MgAMP-PCP on, the conformation of helix 13, which is in good correlation with its, altered mode of phosphate binding and the ensuing increase in the, flexibility of helix 13, as shown by elevated crystallographic B-factors., The possible existence of alternative site(s) for binding of the, nucleotide phosphates may have functional relevance.
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<StructureSection load='1kf0' size='340' side='right'caption='[[1kf0]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1kf0]] is a 1 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=1KF0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KF0 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</scene>, <scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kf0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kf0 OCA], [https://pdbe.org/1kf0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kf0 RCSB], [https://www.ebi.ac.uk/pdbsum/1kf0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kf0 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PGK1_PIG PGK1_PIG]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kf/1kf0_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1kf0 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1KF0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with MG, 3PG and ACP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KF0 OCA].
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*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility., Kovari Z, Flachner B, Naray-Szabo G, Vas M, Biochemistry. 2002 Jul 16;41(28):8796-806. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12102622 12102622]
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[[Category: Large Structures]]
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[[Category: Phosphoglycerate kinase]]
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[[Category: Single protein]]
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[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
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[[Category: Flachner, B.]]
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[[Category: Flachner B]]
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[[Category: Kovari, Z.]]
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[[Category: Kovari Z]]
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[[Category: Naray-Szabo, G.]]
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[[Category: Naray-Szabo G]]
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[[Category: Vas, M.]]
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[[Category: Vas M]]
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[[Category: 3PG]]
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[[Category: ACP]]
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[[Category: MG]]
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[[Category: atp analogue]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:08:45 2007''
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Current revision

Crystal Structure of Pig Muscle Phosphoglycerate Kinase Ternary Complex with AMP-PCP and 3PG

PDB ID 1kf0

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