6dhe

From Proteopedia

(Difference between revisions)

Current revision

RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution

Structural highlights

6dhe is a 20 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Ligands:	, , , , , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSBF_THEVB This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation.[HAMAP-Rule:MF_00643]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Inspired by the period-four oscillation in flash-induced oxygen evolution of photosystem II discovered by Joliot in 1969, Kok performed additional experiments and proposed a five-state kinetic model for photosynthetic oxygen evolution, known as Kok's S-state clock or cycle(1,2). The model comprises four (meta)stable intermediates (S0, S1, S2 and S3) and one transient S4 state, which precedes dioxygen formation occurring in a concerted reaction from two water-derived oxygens bound at an oxo-bridged tetra manganese calcium (Mn4CaO5) cluster in the oxygen-evolving complex(3-7). This reaction is coupled to the two-step reduction and protonation of the mobile plastoquinone QB at the acceptor side of PSII. Here, using serial femtosecond X-ray crystallography and simultaneous X-ray emission spectroscopy with multi-flash visible laser excitation at room temperature, we visualize all (meta)stable states of Kok's cycle as high-resolution structures (2.04-2.08 A). In addition, we report structures of two transient states at 150 and 400 micros, revealing notable structural changes including the binding of one additional 'water', Ox, during the S2-->S3 state transition. Our results suggest that one water ligand to calcium (W3) is directly involved in substrate delivery. The binding of the additional oxygen Ox in the S3 state between Ca and Mn1 supports O-O bond formation mechanisms involving O5 as one substrate, where Ox is either the other substrate oxygen or is perfectly positioned to refill the O5 position during O2 release. Thus, our results exclude peroxo-bond formation in the S3 state, and the nucleophilic attack of W3 onto W2 is unlikely.

Structures of the intermediates of Kok's photosynthetic water oxidation clock.,Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK Nature. 2018 Nov;563(7731):421-425. doi: 10.1038/s41586-018-0681-2. Epub 2018 Nov, 7. PMID:30405241^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Guskov A, Kern J, Gabdulkhakov A, Broser M, Zouni A, Saenger W. Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat Struct Mol Biol. 2009 Mar;16(3):334-42. Epub 2009 Feb 15. PMID:19219048 doi:10.1038/nsmb.1559
↑ Broser M, Gabdulkhakov A, Kern J, Guskov A, Muh F, Saenger W, Zouni A. Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution. J Biol Chem. 2010 Aug 20;285(34):26255-62. Epub 2010 Jun 17. PMID:20558739 doi:10.1074/jbc.M110.127589
↑ Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glockner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371. PMID:25006873 doi:http://dx.doi.org/10.1038/ncomms5371
↑ Kern J, Chatterjee R, Young ID, Fuller FD, Lassalle L, Ibrahim M, Gul S, Fransson T, Brewster AS, Alonso-Mori R, Hussein R, Zhang M, Douthit L, de Lichtenberg C, Cheah MH, Shevela D, Wersig J, Seuffert I, Sokaras D, Pastor E, Weninger C, Kroll T, Sierra RG, Aller P, Butryn A, Orville AM, Liang M, Batyuk A, Koglin JE, Carbajo S, Boutet S, Moriarty NW, Holton JM, Dobbek H, Adams PD, Bergmann U, Sauter NK, Zouni A, Messinger J, Yano J, Yachandra VK. Structures of the intermediates of Kok's photosynthetic water oxidation clock. Nature. 2018 Nov;563(7731):421-425. doi: 10.1038/s41586-018-0681-2. Epub 2018 Nov, 7. PMID:30405241 doi:http://dx.doi.org/10.1038/s41586-018-0681-2

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6dhe"

@@ Line 3: / Line 3: @@
 <StructureSection load='6dhe' size='340' side='right'caption='[[6dhe]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6dhe]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus], [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_(strain_bp-1) Thermosynechococcus elongatus (strain bp-1)] and [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DHE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6dhe]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DHE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8CT:(6R,11cis,11cis,13cis,15cis)-4,5-didehydro-5,6-dihydro-beta,beta-carotene'>8CT</scene>, <scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=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=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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8CT:1,3,3-trimethyl-2-[(1~{E},3~{E},5~{Z},7~{Z},9~{Z},11~{E},13~{Z},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R})-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene'>8CT</scene>, <scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</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=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=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=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </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=6dhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhe OCA], [https://pdbe.org/6dhe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dhe RCSB], [https://www.ebi.ac.uk/pdbsum/6dhe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhe ProSAT]</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=6dhe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhe OCA], [http://pdbe.org/6dhe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhe RCSB], [http://www.ebi.ac.uk/pdbsum/6dhe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhe ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[http://www.uniprot.org/uniprot/PSBB_THEEB PSBB_THEEB]] One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01495]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>  [[http://www.uniprot.org/uniprot/PSBA1_THEEB PSBA1_THEEB]] This is one of the two reaction center proteins of photosystem II. [[http://www.uniprot.org/uniprot/PSBX_THEEB PSBX_THEEB]] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.<ref>PMID:11230572</ref>  [[http://www.uniprot.org/uniprot/CY550_THEEB CY550_THEEB]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. It is not essential for growth under normal conditions but is required under low CO(2) concentrations.[HAMAP-Rule:MF_01378] [[http://www.uniprot.org/uniprot/PSBO_THEEB PSBO_THEEB]] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [[http://www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity).[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBC_THEEB PSBC_THEEB]] One of the components of the core complex of photosystem II (PSII). It binds chlorophyll and helps catalyze the primary light-induced photochemical processes of PSII. PSII is a light-driven water:plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01496]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>  [[http://www.uniprot.org/uniprot/PSBJ_THEEB PSBJ_THEEB]] This protein is a component of the reaction center of photosystem II (By similarity). [[http://www.uniprot.org/uniprot/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref>  [[http://www.uniprot.org/uniprot/PSBU_THEEB PSBU_THEEB]] Stabilizes the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protects the OEC against heat-induced inactivation (By similarity).[HAMAP-Rule:MF_00589] [[http://www.uniprot.org/uniprot/PSBI_THEEB PSBI_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [[http://www.uniprot.org/uniprot/PSBZ_THEEB PSBZ_THEEB]] Controls the interaction of photosystem II (PSII) cores with the light-harvesting antenna. May also aid in binding of PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro.<ref>PMID:17967798</ref>  [[http://www.uniprot.org/uniprot/PSBK_THEEB PSBK_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]
+[https://www.uniprot.org/uniprot/PSBF_THEVB PSBF_THEVB] This b-type cytochrome is tightly associated with the reaction center of photosystem II (PSII). PSII is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation.[HAMAP-Rule:MF_00643]<ref>PMID:19219048</ref> <ref>PMID:20558739</ref> <ref>PMID:25006873</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6dhe" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Photosystem II 3D structures|Photosystem II 3D structures]]
 == References ==
 <references/>
@@ Line 25: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Photosystem II]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[Category: Thermosynechococcus elongatus]]
+[[Category: Adams PD]]
-[[Category: Thermosynechococcus elongatus bp-1]]
+[[Category: Aller P]]
-[[Category: Adams, P D]]
+[[Category: Alonso-Mori R]]
-[[Category: Aller, P]]
+[[Category: Batyuk A]]
-[[Category: Alonso-Mori, R]]
+[[Category: Bergmann U]]
-[[Category: Batyuk, A]]
+[[Category: Boutet S]]
-[[Category: Bergmann, U]]
+[[Category: Brewster AS]]
-[[Category: Boutet, S]]
+[[Category: Butryn A]]
-[[Category: Brewster, A S]]
+[[Category: Carbajo S]]
-[[Category: Butryn, A]]
+[[Category: Chatterjee R]]
-[[Category: Carbajo, S]]
+[[Category: Cheah MH]]
-[[Category: Chatterjee, R]]
+[[Category: Dobbek H]]
-[[Category: Cheah, M H]]
+[[Category: Douthit L]]
-[[Category: Dobbek, H]]
+[[Category: Fransson T]]
-[[Category: Douthit, L]]
+[[Category: Fuller FD]]
-[[Category: Fransson, T]]
+[[Category: Gul S]]
-[[Category: Fuller, F D]]
+[[Category: Holton JM]]
-[[Category: Gul, S]]
+[[Category: Hussein R]]
-[[Category: Holton, J M]]
+[[Category: Ibrahim M]]
-[[Category: Hussein, R]]
+[[Category: Kern J]]
-[[Category: Ibrahim, M]]
+[[Category: Koglin JE]]
-[[Category: Kern, J]]
+[[Category: Kroll T]]
-[[Category: Koglin, J E]]
+[[Category: Lassalle L]]
-[[Category: Kroll, T]]
+[[Category: Liang M]]
-[[Category: Lassalle, L]]
+[[Category: Messinger J]]
-[[Category: Liang, M]]
+[[Category: Moriarty NW]]
-[[Category: Lichtenberg, C de]]
+[[Category: Orville AM]]
-[[Category: Messinger, J]]
+[[Category: Pastor E]]
-[[Category: Moriarty, N W]]
+[[Category: Sauter NK]]
-[[Category: Orville, A M]]
+[[Category: Seufert I]]
-[[Category: Pastor, E]]
+[[Category: Shevela D]]
-[[Category: Sauter, N K]]
+[[Category: Sierra RG]]
-[[Category: Seufert, I]]
+[[Category: Sokaras D]]
-[[Category: Shevela, D]]
+[[Category: Weninger C]]
-[[Category: Sierra, R G]]
+[[Category: Wersig J]]
-[[Category: Sokaras, D]]
+[[Category: Yachandra VK]]
-[[Category: Weninger, C]]
+[[Category: Yano J]]
-[[Category: Wersig, J]]
+[[Category: Young ID]]
-[[Category: Yachandra, V K]]
+[[Category: Zhang M]]
-[[Category: Yano, J]]
+[[Category: Zouni A]]
-[[Category: Young, I D]]
+[[Category: De Lichtenberg C]]
-[[Category: Zhang, M]]
-[[Category: Zouni, A]]
-[[Category: Electron transport]]
-[[Category: Photosynthesis]]
-[[Category: Photosystem]]
-[[Category: Room temperature]]
-[[Category: Transmembrane]]

6dhe

From Proteopedia

Current revision

RT XFEL structure of the dark-stable state of Photosystem II (0F, S1-rich) at 2.05 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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