8gn2: Difference between revisions
New page: '''Unreleased structure''' The entry 8gn2 is ON HOLD Authors: Description: Category: Unreleased Structures |
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The | ==Crystal structure of PPBQ-bound photosystem II complex== | ||
<StructureSection load='8gn2' size='340' side='right'caption='[[8gn2]], [[Resolution|resolution]] 1.95Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8gn2]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermostichus_vulcanus Thermostichus vulcanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GN2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GN2 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HSK:3-HYDROXY-L-HISTIDINE'>HSK</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</scene>, <scene name='pdbligand=K3C:2-phenylcyclohexa-2,5-diene-1,4-dione'>K3C</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=RRX:(3R)-BETA,BETA-CAROTEN-3-OL'>RRX</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=8gn2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gn2 OCA], [https://pdbe.org/8gn2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gn2 RCSB], [https://www.ebi.ac.uk/pdbsum/8gn2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gn2 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/PSBA_THEVL PSBA_THEVL] D1 (PsbA) and D2 (PsbD) bind P680, the primary electron donor of photosystem II (PSII) as well as electron acceptors. PSII is a light-driven water plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01379] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Photosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to Q(B), a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 A resolution. Our results show that all AEAs substitute for Q(B) and are bound to the Q(B)-binding site (Q(B) site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the Q(B) site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone-binding site, designated the Q(D) site, was discovered, which is located in the vicinity of Q(B) site and close to Q(C) site, a binding site reported previously. This Q(D) site is expected to play a role as a channel or a storage site for quinones to be transported to the Q(B) site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of Q(B) in PSII and also provide information for the design of more efficient electron acceptors. | |||
Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.,Kamada S, Nakajima Y, Shen JR J Biol Chem. 2023 May 19;299(7):104839. doi: 10.1016/j.jbc.2023.104839. PMID:37209822<ref>PMID:37209822</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8gn2" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Photosystem II 3D structures|Photosystem II 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermostichus vulcanus]] | |||
[[Category: Kamada S]] | |||
[[Category: Nakajima Y]] | |||
[[Category: Shen J-R]] | |||
Latest revision as of 21:12, 29 November 2023
Crystal structure of PPBQ-bound photosystem II complexCrystal structure of PPBQ-bound photosystem II complex
Structural highlights
FunctionPSBA_THEVL D1 (PsbA) and D2 (PsbD) bind P680, the primary electron donor of photosystem II (PSII) as well as electron acceptors. PSII is a light-driven water plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01379] Publication Abstract from PubMedPhotosystem II (PSII) utilizes light energy to split water, and the electrons extracted from water are transferred to Q(B), a plastoquinone molecule bound to the D1 subunit of PSII. Many artificial electron acceptors (AEAs) with molecular structures similar to that of plastoquinone can accept electrons from PSII. However, the molecular mechanism by which AEAs act on PSII is unclear. Here, we solved the crystal structure of PSII treated with three different AEAs, 2,5-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, and 2-phenyl-1,4-benzoquinone, at 1.95 to 2.10 A resolution. Our results show that all AEAs substitute for Q(B) and are bound to the Q(B)-binding site (Q(B) site) to receive electrons, but their binding strengths are different, resulting in differences in their efficiencies to accept electrons. The acceptor 2-phenyl-1,4-benzoquinone binds most weakly to the Q(B) site and showed the highest oxygen-evolving activity, implying a reverse relationship between the binding strength and oxygen-evolving activity. In addition, a novel quinone-binding site, designated the Q(D) site, was discovered, which is located in the vicinity of Q(B) site and close to Q(C) site, a binding site reported previously. This Q(D) site is expected to play a role as a channel or a storage site for quinones to be transported to the Q(B) site. These results provide the structural basis for elucidating the actions of AEAs and exchange mechanism of Q(B) in PSII and also provide information for the design of more efficient electron acceptors. Structural insights into the action mechanisms of artificial electron acceptors in photosystem II.,Kamada S, Nakajima Y, Shen JR J Biol Chem. 2023 May 19;299(7):104839. doi: 10.1016/j.jbc.2023.104839. PMID:37209822[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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