4rvy

From Proteopedia

(Difference between revisions)

Revision as of 08:30, 8 March 2023

Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)

Structural highlights

4rvy is a 20 chain structure with sequence from Thermosynechococcus vestitus BP-1. This structure supersedes the now removed PDB entry 4q54. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSBA1_THEVB Photosystem II (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. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 A resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.,Kupitz C, Basu S, Grotjohann I, Fromme R, Zatsepin NA, Rendek KN, Hunter MS, Shoeman RL, White TA, Wang D, James D, Yang JH, Cobb DE, Reeder B, Sierra RG, Liu H, Barty A, Aquila AL, Deponte D, Kirian RA, Bari S, Bergkamp JJ, Beyerlein KR, Bogan MJ, Caleman C, Chao TC, Conrad CE, Davis KM, Fleckenstein H, Galli L, Hau-Riege SP, Kassemeyer S, Laksmono H, Liang M, Lomb L, Marchesini S, Martin AV, Messerschmidt M, Milathianaki D, Nass K, Ros A, Roy-Chowdhury S, Schmidt K, Seibert M, Steinbrener J, Stellato F, Yan L, Yoon C, Moore TA, Moore AL, Pushkar Y, Williams GJ, Boutet S, Doak RB, Weierstall U, Frank M, Chapman HN, Spence JC, Fromme P Nature. 2014 Jul 9. doi: 10.1038/nature13453. PMID:25043005^[4]

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
↑ Kupitz C, Basu S, Grotjohann I, Fromme R, Zatsepin NA, Rendek KN, Hunter MS, Shoeman RL, White TA, Wang D, James D, Yang JH, Cobb DE, Reeder B, Sierra RG, Liu H, Barty A, Aquila AL, Deponte D, Kirian RA, Bari S, Bergkamp JJ, Beyerlein KR, Bogan MJ, Caleman C, Chao TC, Conrad CE, Davis KM, Fleckenstein H, Galli L, Hau-Riege SP, Kassemeyer S, Laksmono H, Liang M, Lomb L, Marchesini S, Martin AV, Messerschmidt M, Milathianaki D, Nass K, Ros A, Roy-Chowdhury S, Schmidt K, Seibert M, Steinbrener J, Stellato F, Yan L, Yoon C, Moore TA, Moore AL, Pushkar Y, Williams GJ, Boutet S, Doak RB, Weierstall U, Frank M, Chapman HN, Spence JC, Fromme P. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature. 2014 Jul 9. doi: 10.1038/nature13453. PMID:25043005 doi:http://dx.doi.org/10.1038/nature13453

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/4rvy"

@@ Line 3: / Line 3: @@
 <StructureSection load='4rvy' size='340' side='right'caption='[[4rvy]], [[Resolution|resolution]] 5.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rvy]] is a 38 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4q54 4q54]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RVY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4RVY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rvy]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4q54 4q54]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RVY FirstGlance]. <br>
 </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=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=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=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=4rvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rvy OCA], [https://pdbe.org/4rvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rvy RCSB], [https://www.ebi.ac.uk/pdbsum/4rvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rvy ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4rvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rvy OCA], [http://pdbe.org/4rvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rvy RCSB], [http://www.ebi.ac.uk/pdbsum/4rvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rvy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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/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/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/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[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/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/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/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/PSBA1_THEVB PSBA1_THEVB] Photosystem II (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. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Photosystem II]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[Category: Thermosynechococcus elongatus]]
+[[Category: Aquila A]]
-[[Category: Aquila, A]]
+[[Category: Bari S]]
-[[Category: Bari, S]]
+[[Category: Barty A]]
-[[Category: Barty, A]]
+[[Category: Basu S]]
-[[Category: Basu, S]]
+[[Category: Bergkamp JJ]]
-[[Category: Bergkamp, J J]]
+[[Category: Beyerlein K]]
-[[Category: Beyerlein, K]]
+[[Category: Bogan MJ]]
-[[Category: Bogan, M J]]
+[[Category: Boutet S]]
-[[Category: Boutet, S]]
+[[Category: Caleman C]]
-[[Category: Caleman, C]]
+[[Category: Chao T-C]]
-[[Category: Chao, T C]]
+[[Category: Chapman HN]]
-[[Category: Chapman, H N]]
+[[Category: Cobb DE]]
-[[Category: Cobb, D E]]
+[[Category: Conrad CE]]
-[[Category: Conrad, C E]]
+[[Category: Davis KM]]
-[[Category: Davis, K M]]
+[[Category: Deponte D]]
-[[Category: Deponte, D]]
+[[Category: Doak RB]]
-[[Category: Doak, R B]]
+[[Category: Fleckenstein H]]
-[[Category: Fleckenstein, H]]
+[[Category: Frank M]]
-[[Category: Frank, M]]
+[[Category: Fromme P]]
-[[Category: Fromme, P]]
+[[Category: Fromme R]]
-[[Category: Fromme, R]]
+[[Category: Galli L]]
-[[Category: Galli, L]]
+[[Category: Grotjohann I]]
-[[Category: Grotjohann, I]]
+[[Category: Hau-Riege SP]]
-[[Category: Hau-Riege, S P]]
+[[Category: Hunter M]]
-[[Category: Hunter, M]]
+[[Category: James D]]
-[[Category: James, D]]
+[[Category: Kassemeyer S]]
-[[Category: Kassemeyer, S]]
+[[Category: Kirian R]]
-[[Category: Kirian, R]]
+[[Category: Kupitz C]]
-[[Category: Kupitz, C]]
+[[Category: Laksmono H]]
-[[Category: Laksmono, H]]
+[[Category: Liang M]]
-[[Category: Liang, M]]
+[[Category: Liu H]]
-[[Category: Liu, H]]
+[[Category: Lomb L]]
-[[Category: Lomb, L]]
+[[Category: Marchesini S]]
-[[Category: Marchesini, S]]
+[[Category: Martin AV]]
-[[Category: Martin, A V]]
+[[Category: Messerschmidt M]]
-[[Category: Messerschmidt, M]]
+[[Category: Milathianaki D]]
-[[Category: Milathianaki, D]]
+[[Category: Moore AL]]
-[[Category: Moore, A L]]
+[[Category: Moore TA]]
-[[Category: Moore, T A]]
+[[Category: Nass K]]
-[[Category: Nass, K]]
+[[Category: Pushkar Y]]
-[[Category: Pushkar, Y]]
+[[Category: Reeder B]]
-[[Category: Reeder, B]]
+[[Category: Rendek KN]]
-[[Category: Rendek, K N]]
+[[Category: Ros A]]
-[[Category: Ros, A]]
+[[Category: Roy-Chowdhury S]]
-[[Category: Roy-Chowdhury, S]]
+[[Category: Schmidt K]]
-[[Category: Schmidt, K]]
+[[Category: Seibert M]]
-[[Category: Seibert, M]]
+[[Category: Shoeman RL]]
-[[Category: Shoeman, R L]]
+[[Category: Sierra RG]]
-[[Category: Sierra, R G]]
+[[Category: Spence JCH]]
-[[Category: Spence, J C.H]]
+[[Category: Steinbrener J]]
-[[Category: Steinbrener, J]]
+[[Category: Stellato F]]
-[[Category: Stellato, F]]
+[[Category: Wang D]]
-[[Category: Wang, D]]
+[[Category: Weierstall U]]
-[[Category: Weierstall, U]]
+[[Category: White TA]]
-[[Category: White, T A]]
+[[Category: Williams GJ]]
-[[Category: Williams, G J]]
+[[Category: Yan L]]
-[[Category: Yan, L]]
+[[Category: Yang J-H]]
-[[Category: Yang, J H]]
+[[Category: Yoon C]]
-[[Category: Yoon, C]]
+[[Category: Zatsepin N]]
-[[Category: Zatsepin, N]]
-[[Category: Electron transport]]
-[[Category: Free electron laser]]
-[[Category: Membrane]]
-[[Category: Oxidoreductase]]
-[[Category: Photosystem ii]]
-[[Category: Time resolved]]

4rvy

From Proteopedia

Revision as of 08:30, 8 March 2023

Serial Time resolved crystallography of Photosystem II using a femtosecond X-ray laser. The S state after two flashes (S3)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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