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1a49

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BIS MG-ATP-K-OXALATE COMPLEX OF PYRUVATE KINASE

Structural highlights

1a49 is a 8 chain structure with sequence from Oryctolagus cuniculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KPYM_RABIT Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation (By similarity).

Evolutionary Conservation

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

Publication Abstract from PubMed

Pyruvate kinase from rabbit muscle has been cocrystallized as a complex with MgIIATP, oxalate, Mg2+, and either K+ or Na+. Crystals with either Na+ or K+ belong to the space group P2(1)2(1)2(1), and the asymmetric units contain two tetramers. The structures were solved by molecular replacement and refined to 2.1 (K+) and 2.35 A (Na+) resolution. The structures of the Na+ and K+ complexes are virtually isomorphous. Each of the eight subunits within the asymmetric unit contains MgIIoxalate as a bidentate complex linked to the protein through coordination of Mg2+ to the carboxylates of Glu 271 and Asp 295. Six of the subunits also contain an alpha,beta,gamma-tridentate complex of MgIIATP, and the active-site cleft, located between domains A and B, is closed in these subunits. In the remaining two subunits MgIIATP is missing, and the active-site cleft is open. Closure of the active-site cleft in the fully liganded subunits includes a rotation of 41 degrees of the B domain relative to the A domain. alpha-Carbons of residues in the B domain undergo movements of up to 17.8 A (Lys 124) in the cleft closure. Lys 206, Arg 119, and Asp 177 from the B domain move several angstroms from their positions in the open conformation to contact the MgIIATP complex in the active site. The gamma-phosphate of ATP coordinates to both magnesium ions and to the monovalent cation, K+ or Na+. A Mg2+-coordinated oxygen from the MgIIoxalate complex lies 3.0 A from Pgamma of ATP, and this oxygen is positioned for an in-line attack on the phosphorus. The side chains of Lys 269 and Arg 119 are positioned to provide leaving-group activation in the forward and reverse directions. There is no obvious candidate for the acid/base catalyst near the 2-si face of the prospective enolate of the normal substrate. A functional group linked through solvent and side-chain hydroxyls may function in a proton relay.

Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel.,Larsen TM, Benning MM, Rayment I, Reed GH Biochemistry. 1998 May 5;37(18):6247-55. PMID:9572839^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Larsen TM, Benning MM, Rayment I, Reed GH. Structure of the bis(Mg2+)-ATP-oxalate complex of the rabbit muscle pyruvate kinase at 2.1 A resolution: ATP binding over a barrel. Biochemistry. 1998 May 5;37(18):6247-55. PMID:9572839 doi:http://dx.doi.org/10.1021/bi980243s

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1a49"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[1a49]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A49 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</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=1a49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a49 OCA], [https://pdbe.org/1a49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a49 RCSB], [https://www.ebi.ac.uk/pdbsum/1a49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a49 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/KPYM_RABIT KPYM_RABIT]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation (By similarity).
+[https://www.uniprot.org/uniprot/KPYM_RABIT KPYM_RABIT] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation (By similarity).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 38: @@
 [[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Pyruvate kinase]]
+[[Category: Benning MM]]
-[[Category: Benning, M M]]
+[[Category: Larsen TM]]
-[[Category: Larsen, T M]]
+[[Category: Rayment I]]
-[[Category: Rayment, I]]
+[[Category: Reed GH]]
-[[Category: Reed, G H]]
-[[Category: Domain movement]]
-[[Category: Potassium binding]]
-[[Category: Rabbit muscle]]
-[[Category: Transferase]]

1a49

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Current revision

BIS MG-ATP-K-OXALATE COMPLEX OF PYRUVATE KINASE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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