6w1r

From Proteopedia

(Difference between revisions)

Revision as of 07:45, 1 July 2020

RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution

Structural highlights

6w1r is a 40 chain structure with sequence from Thermosynechococcus elongatus (strain bp-1). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , , , , , , , ,
NonStd Res:
Related:	6w1p, 6w1o, 6w1q, 6w1t, 6w1u, 6w1v
Activity:	Photosystem II, with EC number 1.10.3.9
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [PSBL_THEEB] Required for PSII activity (By similarity). [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]^[1] ^[2] ^[3] [PSBJ_THEEB] This protein is a component of the reaction center of photosystem II (By similarity). [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]^[4] ^[5] ^[6] [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] [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.^[7] [PSBT_THEEB] Seems to play a role in the dimerization of PSII.^[8] [PSBI_THEEB] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [PSBA1_THEEB] This is one of the two reaction center proteins of photosystem II. [PSBX_THEEB] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.^[9] [YCF12_THEEB] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [PSBK_THEEB] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [PSBO_THEEB] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [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] [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]

Publication Abstract from PubMed

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S1, S2, S3, and S0, showing that a water molecule is inserted during the S2 --> S3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S2 --> S3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, QA and QB, are observed. At the donor site, tyrosine YZ and His190 H-bonded to it move by 50 micros after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of OX(H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a "water wheel"-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (tau of approximately 350 micros) during the S2 --> S3 transition mirrors the appearance of OX electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

Untangling the sequence of events during the S2 --> S3 transition in photosystem II and implications for the water oxidation mechanism.,Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J Proc Natl Acad Sci U S A. 2020 May 20. pii: 2000529117. doi:, 10.1073/pnas.2000529117. PMID:32434915^[10]

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

References

↑ 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
↑ Broser M, Glockner C, Gabdulkhakov A, Guskov A, Buchta J, Kern J, Muh F, Dau H, Saenger W, Zouni A. Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn. J Biol Chem. 2011 May 6;286(18):15964-72. Epub 2011 Mar 2. PMID:21367867 doi:http://dx.doi.org/10.1074/jbc.M110.215970
↑ 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
↑ 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
↑ Broser M, Glockner C, Gabdulkhakov A, Guskov A, Buchta J, Kern J, Muh F, Dau H, Saenger W, Zouni A. Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn. J Biol Chem. 2011 May 6;286(18):15964-72. Epub 2011 Mar 2. PMID:21367867 doi:http://dx.doi.org/10.1074/jbc.M110.215970
↑ 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
↑ Iwai M, Suzuki T, Dohmae N, Inoue Y, Ikeuchi M. Absence of the PsbZ subunit prevents association of PsbK and Ycf12 with the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Plant Cell Physiol. 2007 Dec;48(12):1758-63. Epub 2007 Oct 28. PMID:17967798 doi:pcm148
↑ Iwai M, Katoh H, Katayama M, Ikeuchi M. PSII-Tc protein plays an important role in dimerization of photosystem II. Plant Cell Physiol. 2004 Dec;45(12):1809-16. PMID:15653799 doi:45/12/1809
↑ Katoh H, Ikeuchi M. Targeted disruption of psbX and biochemical characterization of photosystem II complex in the thermophilic cyanobacterium Synechococcus elongatus. Plant Cell Physiol. 2001 Feb;42(2):179-88. PMID:11230572
↑ Ibrahim M, Fransson T, Chatterjee R, Cheah MH, Hussein R, Lassalle L, Sutherlin KD, Young ID, Fuller FD, Gul S, Kim IS, Simon PS, de Lichtenberg C, Chernev P, Bogacz I, Pham CC, Orville AM, Saichek N, Northen T, Batyuk A, Carbajo S, Alonso-Mori R, Tono K, Owada S, Bhowmick A, Bolotovsky R, Mendez D, Moriarty NW, Holton JM, Dobbek H, Brewster AS, Adams PD, Sauter NK, Bergmann U, Zouni A, Messinger J, Kern J, Yachandra VK, Yano J. Untangling the sequence of events during the S2 --> S3 transition in photosystem II and implications for the water oxidation mechanism. Proc Natl Acad Sci U S A. 2020 May 20. pii: 2000529117. doi:, 10.1073/pnas.2000529117. PMID:32434915 doi:http://dx.doi.org/10.1073/pnas.2000529117

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6w1r"

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 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[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/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/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/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/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/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref>  [[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/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[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]
+[[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/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[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/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/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/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/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref>  [[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/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/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[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/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/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/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]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

6w1r

From Proteopedia

Revision as of 07:45, 1 July 2020

RT XFEL structure of Photosystem II 150 microseconds after the second illumination at 2.23 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

References

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