6ln3
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==Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP== | ==Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP== | ||
| - | <StructureSection load='6ln3' size='340' side='right'caption='[[6ln3]]' scene=''> | + | <StructureSection load='6ln3' size='340' side='right'caption='[[6ln3]], [[Resolution|resolution]] 2.00Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LN3 OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[6ln3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LN3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LN3 FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6ln3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ln3 OCA], [https://pdbe.org/6ln3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ln3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ln3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ln3 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/KADA_AERPE KADA_AERPE] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 A. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and gamma-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the beta-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino acid residues for the catalysis of ADK. | ||
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| + | Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP.,Shibanuma Y, Nemoto N, Yamamoto N, Sampei GI, Kawai G J Biochem. 2020 Apr 9. pii: 5818497. doi: 10.1093/jb/mvaa043. PMID:32271910<ref>PMID:32271910</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6ln3" style="background-color:#fffaf0;"></div> | ||
| + | |||
| + | ==See Also== | ||
| + | *[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Aeropyrum pernix K1]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Kawai G]] | [[Category: Kawai G]] | ||
Current revision
Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP
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