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| | <StructureSection load='4jlb' size='340' side='right'caption='[[4jlb]], [[Resolution|resolution]] 1.53Å' scene=''> | | <StructureSection load='4jlb' size='340' side='right'caption='[[4jlb]], [[Resolution|resolution]] 1.53Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jlb]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquae Aquae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JLB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jlb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JLB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jl5|4jl5]], [[4jla|4jla]], [[4jld|4jld]], [[4jlo|4jlo]], [[4jlp|4jlp]]</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=4jlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jlb OCA], [https://pdbe.org/4jlb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jlb RCSB], [https://www.ebi.ac.uk/pdbsum/4jlb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jlb ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adk, aq_078 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224324 AQUAE])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylate_kinase Adenylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.3 2.7.4.3] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4jlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jlb OCA], [http://pdbe.org/4jlb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jlb RCSB], [http://www.ebi.ac.uk/pdbsum/4jlb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jlb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity). | + | [https://www.uniprot.org/uniprot/KAD_AQUAE KAD_AQUAE] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adenylate kinase]] | + | [[Category: Aquifex aeolicus VF5]] |
| - | [[Category: Aquae]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cho, Y J]] | + | [[Category: Cho Y-J]] |
| - | [[Category: Kern, D]] | + | [[Category: Kern D]] |
| - | [[Category: Adp binding]]
| + | |
| - | [[Category: Phosphoryl transfer reaction]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
KAD_AQUAE Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. This small ubiquitous enzyme involved in the energy metabolism and nucleotide synthesis, is essential for maintenance and cell growth (By similarity).
Publication Abstract from PubMed
Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg2+ cofactor activates two distinct molecular events: phosphoryl transfer (>105-fold) and lid opening (103-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 103-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site.
The energy landscape of adenylate kinase during catalysis.,Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D Nat Struct Mol Biol. 2015 Jan 12. doi: 10.1038/nsmb.2941. PMID:25580578[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kerns SJ, Agafonov RV, Cho YJ, Pontiggia F, Otten R, Pachov DV, Kutter S, Phung LA, Murphy PN, Thai V, Alber T, Hagan MF, Kern D. The energy landscape of adenylate kinase during catalysis. Nat Struct Mol Biol. 2015 Jan 12. doi: 10.1038/nsmb.2941. PMID:25580578 doi:http://dx.doi.org/10.1038/nsmb.2941
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