7rf1

From Proteopedia

(Difference between revisions)

Current revision

RT XFEL structure of Photosystem II averaged across all S-states at 1.89 Angstrom resolution

Structural highlights

7rf1 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 1.89Å
Ligands:	, , , , , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSBU_THEVB One of the extrinsic, lumenal subunits of photosystem II (PSII). 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. The extrinsic proteins stabilize the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protect the OEC against heat-induced inactivation.[HAMAP-Rule:MF_00589]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 A structure obtained by averaging all the S states and refining the data of various time points during the S(2) to S(3) transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.

Structural dynamics in the water and proton channels of photosystem II during the S(2) to S(3) transition.,Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J Nat Commun. 2021 Nov 11;12(1):6531. doi: 10.1038/s41467-021-26781-z. PMID:34764256^[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
↑ Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J. Structural dynamics in the water and proton channels of photosystem II during the S(2) to S(3) transition. Nat Commun. 2021 Nov 11;12(1):6531. PMID:34764256 doi:10.1038/s41467-021-26781-z

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/7rf1"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7rf1 is ON HOLD  until Paper Publication
+==RT XFEL structure of Photosystem II averaged across all S-states at 1.89 Angstrom resolution==
+<StructureSection load='7rf1' size='340' side='right'caption='[[7rf1]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7rf1]] 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=7RF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RF1 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]] 1.89&#8491;</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=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>, <scene name='pdbligand=STE:STEARIC+ACID'>STE</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=7rf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rf1 OCA], [https://pdbe.org/7rf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rf1 RCSB], [https://www.ebi.ac.uk/pdbsum/7rf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rf1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSBU_THEVB PSBU_THEVB] One of the extrinsic, lumenal subunits of photosystem II (PSII). 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. The extrinsic proteins stabilize the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protect the OEC against heat-induced inactivation.[HAMAP-Rule:MF_00589]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 A structure obtained by averaging all the S states and refining the data of various time points during the S(2) to S(3) transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.
-Authors:
+Structural dynamics in the water and proton channels of photosystem II during the S(2) to S(3) transition.,Hussein R, Ibrahim M, Bhowmick A, Simon PS, Chatterjee R, Lassalle L, Doyle M, Bogacz I, Kim IS, Cheah MH, Gul S, de Lichtenberg C, Chernev P, Pham CC, Young ID, Carbajo S, Fuller FD, Alonso-Mori R, Batyuk A, Sutherlin KD, Brewster AS, Bolotovsky R, Mendez D, Holton JM, Moriarty NW, Adams PD, Bergmann U, Sauter NK, Dobbek H, Messinger J, Zouni A, Kern J, Yachandra VK, Yano J Nat Commun. 2021 Nov 11;12(1):6531. doi: 10.1038/s41467-021-26781-z. PMID:34764256<ref>PMID:34764256</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7rf1" 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: Large Structures]]
+[[Category: Thermosynechococcus vestitus BP-1]]
+[[Category: Adams PD]]
+[[Category: Alonso-Mori R]]
+[[Category: Batyuk A]]
+[[Category: Bergmann U]]
+[[Category: Bhowmick A]]
+[[Category: Bogacz I]]
+[[Category: Bolotovski R]]
+[[Category: Brewster AS]]
+[[Category: Carbajo S]]
+[[Category: Chatterjee R]]
+[[Category: Cheah MH]]
+[[Category: Chernev P]]
+[[Category: Dobbek H]]
+[[Category: Doyle MD]]
+[[Category: Fuller FD]]
+[[Category: Gul S]]
+[[Category: Holton JM]]
+[[Category: Hussein R]]
+[[Category: Ibrahim M]]
+[[Category: Kern J]]
+[[Category: Kim I-S]]
+[[Category: Lassalle L]]
+[[Category: Mendez D]]
+[[Category: Messinger J]]
+[[Category: Moriarty NW]]
+[[Category: Pham CC]]
+[[Category: Sauter NK]]
+[[Category: Simon PS]]
+[[Category: Sutherlin KD]]
+[[Category: Yachandra VK]]
+[[Category: Yano J]]
+[[Category: Young ID]]
+[[Category: Zouni A]]
+[[Category: De Lichtenberg C]]

7rf1

From Proteopedia

Current revision

RT XFEL structure of Photosystem II averaged across all S-states at 1.89 Angstrom resolution

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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