3nbf: Difference between revisions
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<StructureSection load='3nbf' size='340' side='right'caption='[[3nbf]], [[Resolution|resolution]] 1.90Å' scene=''> | <StructureSection load='3nbf' size='340' side='right'caption='[[3nbf]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3nbf]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3nbf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NBF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8OD:[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>8OD</scene>, <scene name='pdbligand=8OP:[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8OP</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OD:[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+PHOSPHONO+HYDROGEN+PHOSPHATE'>8OD</scene>, <scene name='pdbligand=8OP:[(2R,3S,4R,5R)-5-(6-AZANYL-8-OXO-7H-PURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8OP</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3nbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nbf OCA], [https://pdbe.org/3nbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nbf RCSB], [https://www.ebi.ac.uk/pdbsum/3nbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nbf ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q72GF3_THET2 Q72GF3_THET2] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermus thermophilus HB27]] | ||
[[Category: Klostermeier | [[Category: Klostermeier D]] | ||
[[Category: Rudolph | [[Category: Rudolph MG]] | ||
Latest revision as of 19:45, 1 November 2023
Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADPQ28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP
Structural highlights
FunctionPublication Abstract from PubMedAbstract DEAD-box proteins disrupt or remodel RNA and protein/RNA complexes at the expense of ATP. The catalytic core is composed of two flexibly connected RecA-like domains. The N-terminal domain contains most of the motifs involved in nucleotide binding and serves as a minimalistic model for helicase/nucleotide interactions. A single conserved glutamine in the so-called Q-motif has been suggested as a conformational sensor for the nucleotide state. To reprogram the Thermus thermophilus RNA helicase Hera for use of oxo-ATP instead of ATP and to investigate the sensor function of the Q-motif, we analyzed helicase activity of Hera Q28E. Crystal structures of the Hera N-terminal domain Q28E mutant (TthDEAD_Q28E) in apo- and ligand-bound forms show that Q28E does change specificity from adenine to 8-oxoadenine. However, significant structural changes accompany the Q28E mutation, which prevent the P-loop from adopting its catalytically active conformation and explain the lack of helicase activity of Hera_Q28E with either ATP or 8-oxo-ATP as energy sources. 8-Oxo-adenosine, 8-oxo-AMP, and 8-oxo-ADP weakly bind to TthDEAD_Q28E but in non-canonical modes. These results indicate that the Q-motif not only senses the nucleotide state of the helicase but could also stabilize a catalytically competent conformation of the P-loop and other helicase signature motifs. Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.,Strohmeier J, Hertel I, Diederichsen U, Rudolph MG, Klostermeier D Biol Chem. 2011 Apr;392(4):357-69. PMID:21391900[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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