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| | ==New structural conformations of adenylate kinase from Streptococcus pneumoniae D39 with Ap5A== | | ==New structural conformations of adenylate kinase from Streptococcus pneumoniae D39 with Ap5A== |
| - | <StructureSection load='4w5j' size='340' side='right' caption='[[4w5j]], [[Resolution|resolution]] 1.65Å' scene=''> | + | <StructureSection load='4w5j' size='340' side='right'caption='[[4w5j]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4w5j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Strp2 Strp2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W5J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W5J FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4w5j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_D39 Streptococcus pneumoniae D39]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W5J FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AP5:BIS(ADENOSINE)-5-PENTAPHOSPHATE'>AP5</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4nu0|4nu0]], [[4w5h|4w5h]]</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=4w5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w5j OCA], [https://pdbe.org/4w5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w5j RCSB], [https://www.ebi.ac.uk/pdbsum/4w5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w5j ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adk, SPD_0214 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=373153 STRP2])</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=4w5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w5j OCA], [http://pdbe.org/4w5j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w5j RCSB], [http://www.ebi.ac.uk/pdbsum/4w5j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w5j ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KAD_STRP2 KAD_STRP2]] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity). | + | [https://www.uniprot.org/uniprot/KAD_STRP2 KAD_STRP2] Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4w5j" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4w5j" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Adenylate kinase 3D structures|Adenylate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Adenylate kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Strp2]] | + | [[Category: Streptococcus pneumoniae D39]] |
| - | [[Category: Lee, S H]] | + | [[Category: Lee SH]] |
| - | [[Category: Thach, T T]] | + | [[Category: Thach TT]] |
| - | [[Category: Amp/atp binding]]
| + | |
| - | [[Category: Nmp/lid domain]]
| + | |
| - | [[Category: Phosphotransferase]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
KAD_STRP2 Catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. Plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism (By similarity).
Publication Abstract from PubMed
Adenylate kinases (AdKs; EC 2.7.3.4) play a critical role in intercellular homeostasis by the interconversion of ATP and AMP to two ADP molecules. Crystal structures of adenylate kinase from Streptococcus pneumoniae D39 (SpAdK) have recently been determined using ligand-free and inhibitor-bound crystals belonging to space groups P21 and P1, respectively. Here, new crystal structures of SpAdK in ligand-free and inhibitor-bound states determined at 1.96 and 1.65 A resolution, respectively, are reported. The new ligand-free crystal belonged to space group C2, with unit-cell parameters a = 73.5, b = 54.3, c = 62.7 A, beta = 118.8 degrees . The new ligand-free structure revealed an open conformation that differed from the previously determined conformation, with an r.m.s.d on C(alpha) atoms of 1.4 A. The new crystal of the complex with the two-substrate-mimicking inhibitor P(1),P(5)-bis(adenosine-5'-)pentaphosphate (Ap5A) belonged to space group P1, with unit-cell parameters a = 53.9, b = 62.3, c = 63.0 A, alpha = 101.9, beta = 112.6, gamma = 89.9 degrees . Despite belonging to the same space group as the previously reported crystal, the new Ap5A-bound crystal contains four molecules in the asymmetric unit, compared with two in the previous crystal, and shows slightly different lattice contacts. These results demonstrate that SpAdK can crystallize promiscuously in different forms and that the open structure is flexible in conformation.
New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations.,Thach TT, Lee S Acta Crystallogr F Struct Biol Commun. 2014 Nov;70(Pt 11):1468-71. doi:, 10.1107/S2053230X14020718. Epub 2014 Oct 25. PMID:25372811[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Thach TT, Lee S. New crystal structures of adenylate kinase from Streptococcus pneumoniae D39 in two conformations. Acta Crystallogr F Struct Biol Commun. 2014 Nov;70(Pt 11):1468-71. doi:, 10.1107/S2053230X14020718. Epub 2014 Oct 25. PMID:25372811 doi:http://dx.doi.org/10.1107/S2053230X14020718
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