7f8t: Difference between revisions
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<StructureSection load='7f8t' size='340' side='right'caption='[[7f8t]], [[Resolution|resolution]] 1.50Å' scene=''> | <StructureSection load='7f8t' size='340' side='right'caption='[[7f8t]], [[Resolution|resolution]] 1.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7f8t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F8T FirstGlance]. <br> | <table><tr><td colspan='2'>[[7f8t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanosarcina_mazei Methanosarcina mazei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7F8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7F8T FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.5Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7f8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f8t OCA], [https://pdbe.org/7f8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f8t RCSB], [https://www.ebi.ac.uk/pdbsum/7f8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f8t ProSAT]</span></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=7f8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7f8t OCA], [https://pdbe.org/7f8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7f8t RCSB], [https://www.ebi.ac.uk/pdbsum/7f8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7f8t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8PYK9_METMA Q8PYK9_METMA] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
Flavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD(*-) isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge allows proton transfer from arginine to FAD(*-). Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis. | |||
Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme.,Maestre-Reyna M, Yang CH, Nango E, Huang WC, Ngurah Putu EPG, Wu WJ, Wang PH, Franz-Badur S, Saft M, Emmerich HJ, Wu HY, Lee CC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Sugahara M, Owada S, Hosokawa Y, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Hsu KC, Kiontke S, Schapiro I, Spadaccini R, Royant A, Yamamoto J, Iwata S, Essen LO, Bessho Y, Tsai MD Nat Chem. 2022 Apr 7. pii: 10.1038/s41557-022-00922-3. doi:, 10.1038/s41557-022-00922-3. PMID:35393554<ref>PMID:35393554</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bessho | [[Category: Methanosarcina mazei]] | ||
[[Category: Chang | [[Category: Bessho Y]] | ||
[[Category: Essen | [[Category: Chang Y-K]] | ||
[[Category: Franz-Badur | [[Category: Essen L-O]] | ||
[[Category: Gusti-Ngurah-Putu | [[Category: Franz-Badur S]] | ||
[[Category: Huang | [[Category: Gusti-Ngurah-Putu E-P]] | ||
[[Category: Huang | [[Category: Huang K-F]] | ||
[[Category: Iwata | [[Category: Huang WC]] | ||
[[Category: Joti | [[Category: Iwata S]] | ||
[[Category: Kiontke | [[Category: Joti Y]] | ||
[[Category: Lee | [[Category: Kiontke S]] | ||
[[Category: Liao | [[Category: Lee C-C]] | ||
[[Category: Maestre-Reyna | [[Category: Liao J-H]] | ||
[[Category: Nango | [[Category: Maestre-Reyna M]] | ||
[[Category: Owada | [[Category: Nango E]] | ||
[[Category: Sugahara | [[Category: Owada S]] | ||
[[Category: Tanaka | [[Category: Sugahara M]] | ||
[[Category: Tono | [[Category: Tanaka R]] | ||
[[Category: Tsai | [[Category: Tono K]] | ||
[[Category: Wang | [[Category: Tsai M-D]] | ||
[[Category: Weng | [[Category: Wang P-H]] | ||
[[Category: Wu | [[Category: Weng J-H]] | ||
[[Category: Wu | [[Category: Wu H-Y]] | ||
[[Category: Yamamoto | [[Category: Wu W-J]] | ||
[[Category: Yang | [[Category: Yamamoto J]] | ||
[[Category: Yang C-H]] | |||
Latest revision as of 20:11, 29 November 2023
Re-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazeiRe-refinement of the 2XRY X-ray structure of archaeal class II CPD photolyase from Methanosarcina mazei
Structural highlights
FunctionPublication Abstract from PubMedFlavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD(*-) isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge allows proton transfer from arginine to FAD(*-). Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis. Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme.,Maestre-Reyna M, Yang CH, Nango E, Huang WC, Ngurah Putu EPG, Wu WJ, Wang PH, Franz-Badur S, Saft M, Emmerich HJ, Wu HY, Lee CC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Sugahara M, Owada S, Hosokawa Y, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Hsu KC, Kiontke S, Schapiro I, Spadaccini R, Royant A, Yamamoto J, Iwata S, Essen LO, Bessho Y, Tsai MD Nat Chem. 2022 Apr 7. pii: 10.1038/s41557-022-00922-3. doi:, 10.1038/s41557-022-00922-3. PMID:35393554[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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