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4pbu

From Proteopedia

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Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state

Structural highlights

4pbu 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 5Å
Ligands:	, , , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSBH_THEVB One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. 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_00752]^[1] ^[2] ^[3] ^[4]

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^[5]

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

References

↑ Iwai M, Katayama M, Ikeuchi M. Absence of the psbH gene product destabilizes the Photosystem II complex and prevents association of the Photosystem II-X protein in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Photosynth Res. 2006 Mar;87(3):313-22. PMID:16699922 doi:10.1007/s11120-005-9013-0
↑ 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/4pbu"

@@ Line 1: / Line 1: @@
 ==Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state==
-<StructureSection load='4pbu' size='340' side='right' caption='[[4pbu]], [[Resolution|resolution]] 5.00&Aring;' scene=''>
+<StructureSection load='4pbu' size='340' side='right'caption='[[4pbu]], [[Resolution|resolution]] 5.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4pbu]] is a 38 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PBU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4pbu]] 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=4PBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PBU FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=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><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]] 5&#8491;</td></tr>
-<tr><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='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=MG:MAGNESIUM+ION'>MG</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pbu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4pbu RCSB], [http://www.ebi.ac.uk/pdbsum/4pbu PDBsum]</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=4pbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pbu OCA], [https://pdbe.org/4pbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pbu RCSB], [https://www.ebi.ac.uk/pdbsum/4pbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pbu ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSBH_THEVB PSBH_THEVB] One of the components of the core complex of photosystem II (PSII), required for its stability and/or assembly. 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_00752]<ref>PMID:16699922</ref> <ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>
+<div style="background-color:#fffaf0;">
+== 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<ref>PMID:25043005</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4pbu" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
+*[[Photosystem II 3D structures|Photosystem II 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Photosystem II]]
+[[Category: Large Structures]]
-[[Category: Thermosynechococcus elongatus]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[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, J J.]]
+[[Category: Bergkamp JJ]]
-[[Category: Beyerlein, K]]
+[[Category: Beyerlein K]]
-[[Category: Bogan, M J.]]
+[[Category: Bogan MJ]]
-[[Category: Boutet, S.]]
+[[Category: Boutet S]]
-[[Category: Caleman, C.]]
+[[Category: Caleman C]]
-[[Category: Chao, T-C.]]
+[[Category: Chao T-C]]
-[[Category: Chapman, H N.]]
+[[Category: Chapman HN]]
-[[Category: Cobb, D E.]]
+[[Category: Cobb DE]]
-[[Category: Conrad, C E.]]
+[[Category: Conrad CE]]
-[[Category: Davis, K M.]]
+[[Category: Davis KM]]
-[[Category: Deponte, D.]]
+[[Category: Deponte D]]
-[[Category: Doak, R B.]]
+[[Category: Doak RB]]
-[[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, S P.]]
+[[Category: Hau-Riege SP]]
-[[Category: Hunter, M.]]
+[[Category: Hunter M]]
-[[Category: James, D.]]
+[[Category: James D]]
-[[Category: Kassemeyer, S.]]
+[[Category: Kassemeyer S]]
-[[Category: Kirian, R A.]]
+[[Category: Kirian RA]]
-[[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, A V.]]
+[[Category: Martin AV]]
-[[Category: Messerschmidt, M.]]
+[[Category: Messerschmidt M]]
-[[Category: Milathianaki, D.]]
+[[Category: Milathianaki D]]
-[[Category: Moore, A L.]]
+[[Category: Moore AL]]
-[[Category: Moore, T A.]]
+[[Category: Moore TA]]
-[[Category: Nass, K.]]
+[[Category: Nass K]]
-[[Category: Pushkar, Y.]]
+[[Category: Pushkar Y]]
-[[Category: Reeder,B.]]
+[[Category: Reeder B]]
-[[Category: Rendek, K N.]]
+[[Category: Rendek KN]]
-[[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, R L.]]
+[[Category: Shoeman RL]]
-[[Category: Sierra, R G.]]
+[[Category: Sierra RG]]
-[[Category: Spence, J C.H.]]
+[[Category: Spence JCH]]
-[[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, T A.]]
+[[Category: White TA]]
-[[Category: Williams, G J.]]
+[[Category: Williams GJ]]
-[[Category: Yan, L.]]
+[[Category: Yan L]]
-[[Category: Yang, J-H.]]
+[[Category: Yang JH]]
-[[Category: Yoon, C.]]
+[[Category: Yoon C]]
-[[Category: Zatsepin, N.]]
+[[Category: Zatsepin N]]
-[[Category: Free electron laser]]
-[[Category: Photosynthesis]]
-[[Category: Photosystem ii]]
-[[Category: Time resolved]]

4pbu

From Proteopedia

Current revision

Serial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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