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[[Image:4il6.jpg|left|200px]]
==Structure of Sr-substituted photosystem II==
<StructureSection load='4il6' size='340' side='right' caption='[[4il6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4il6]] is a 39 chain structure with sequence from [http://en.wikipedia.org/wiki/Theeb Theeb] and [http://en.wikipedia.org/wiki/Thermosynechococcus_vulcanus Thermosynechococcus vulcanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IL6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IL6 FirstGlance]. <br>
</td></tr><tr id='ligand'><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=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=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</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=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OER:SR-MN4-O5+CLUSTER'>OER</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>
<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='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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4il6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4il6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4il6 RCSB], [http://www.ebi.ac.uk/pdbsum/4il6 PDBsum]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/PSBL_THEVL PSBL_THEVL]] This protein is a component of the reaction center 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.[HAMAP-Rule:MF_01317] [[http://www.uniprot.org/uniprot/PSBA_THEVL PSBA_THEVL]] D1 (PsbA) and D2 (PsbD) bind P680, the primary electron donor of photosystem II (PSII) as well as electron acceptors. 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.[HAMAP-Rule:MF_01379] [[http://www.uniprot.org/uniprot/CY550_THEVL CY550_THEVL]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II (PSII). Binds to PSII in the absence of other extrinsic proteins; required for binding of the PsbU protein to photosystem II. In PSII particles without oxygen-evolving activity, maximal activity is restored only by binding of cytochrome c550, PsbU and the 33 kDa PsbO protein. 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.<ref>PMID:1314738</ref> <ref>PMID:8382523</ref>  [[http://www.uniprot.org/uniprot/PSBF_THEVL PSBF_THEVL]] This b-type cytochrome is tightly associated with the reaction center 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.[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBJ_THEVL PSBJ_THEVL]] This protein is a component of the reaction center 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.[HAMAP-Rule:MF_01305] [[http://www.uniprot.org/uniprot/PSBT_THEVL PSBT_THEVL]] Seems to play a role in the dimerization 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.[HAMAP-Rule:MF_00808] [[http://www.uniprot.org/uniprot/PSBE_THEVL PSBE_THEVL]] This b-type cytochrome is tightly associated with the reaction center 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.[HAMAP-Rule:MF_00642]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (MnCaO) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca in this cluster and the possible location of water substrates in this process, we crystallized Sr-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 A, and compared it with the 1.9 A structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the MnCaO-cluster relative to that of Ca, resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca, W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 A structure of native PSII, was found in the Sr-PSII structure.


{{STRUCTURE_4il6|  PDB=4il6  |  SCENE=  }}
Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation.,Koua FH, Umena Y, Kawakami K, Shen JR Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3889-94. doi:, 10.1073/pnas.1219922110. Epub 2013 Feb 20. PMID:23426624<ref>PMID:23426624</ref>


===Structure of Sr-substituted photosystem II===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


 
==See Also==
==About this Structure==
*[[Photosystem II|Photosystem II]]
[[4il6]] is a 39 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_bp-1 Thermosynechococcus elongatus bp-1] and [http://en.wikipedia.org/wiki/Thermosynechococcus_vulcanus Thermosynechococcus vulcanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IL6 OCA].
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Photosystem II]]
[[Category: Photosystem II]]
[[Category: Thermosynechococcus elongatus bp-1]]
[[Category: Theeb]]
[[Category: Thermosynechococcus vulcanus]]
[[Category: Thermosynechococcus vulcanus]]
[[Category: Kamiya, N.]]
[[Category: Kamiya, N]]
[[Category: Kawakami, K.]]
[[Category: Kawakami, K]]
[[Category: Koua, F H.M.]]
[[Category: Koua, F H.M]]
[[Category: Shen, J R.]]
[[Category: Shen, J R]]
[[Category: Umena, Y.]]
[[Category: Umena, Y]]
[[Category: Electron transfer]]
[[Category: Electron transfer]]
[[Category: Electron transport]]
[[Category: Electron transport]]

Revision as of 11:50, 15 February 2015

Structure of Sr-substituted photosystem IIStructure of Sr-substituted photosystem II

Structural highlights

4il6 is a 39 chain structure with sequence from Theeb and Thermosynechococcus vulcanus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , , , , , , , , , , , , , , , ,
NonStd Res:
Activity:Photosystem II, with EC number 1.10.3.9
Resources:FirstGlance, OCA, RCSB, PDBsum

Function

[PSBL_THEVL] This protein is a component of the reaction center 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.[HAMAP-Rule:MF_01317] [PSBA_THEVL] D1 (PsbA) and D2 (PsbD) bind P680, the primary electron donor of photosystem II (PSII) as well as electron acceptors. 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.[HAMAP-Rule:MF_01379] [CY550_THEVL] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II (PSII). Binds to PSII in the absence of other extrinsic proteins; required for binding of the PsbU protein to photosystem II. In PSII particles without oxygen-evolving activity, maximal activity is restored only by binding of cytochrome c550, PsbU and the 33 kDa PsbO protein. 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.[1] [2] [PSBF_THEVL] This b-type cytochrome is tightly associated with the reaction center 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.[HAMAP-Rule:MF_00643] [PSBJ_THEVL] This protein is a component of the reaction center 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.[HAMAP-Rule:MF_01305] [PSBT_THEVL] Seems to play a role in the dimerization 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.[HAMAP-Rule:MF_00808] [PSBE_THEVL] This b-type cytochrome is tightly associated with the reaction center 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.[HAMAP-Rule:MF_00642]

Publication Abstract from PubMed

Oxygen-evolving complex of photosystem II (PSII) is a tetra-manganese calcium penta-oxygenic cluster (MnCaO) catalyzing light-induced water oxidation through several intermediate states (S-states) by a mechanism that is not fully understood. To elucidate the roles of Ca in this cluster and the possible location of water substrates in this process, we crystallized Sr-substituted PSII from Thermosynechococcus vulcanus, analyzed its crystal structure at a resolution of 2.1 A, and compared it with the 1.9 A structure of native PSII. Our analysis showed that the position of Sr was moved toward the outside of the cubane structure of the MnCaO-cluster relative to that of Ca, resulting in a general elongation of the bond distances between Sr and its surrounding atoms compared with the corresponding distances in the Ca-containing cluster. In particular, we identified an apparent elongation in the bond distance between Sr and one of the two terminal water ligands of Ca, W3, whereas that of the Sr-W4 distance was not much changed. This result may contribute to the decrease of oxygen evolution upon Sr-substitution, and suggests a weak binding and rather mobile nature of this particular water molecule (W3), which in turn implies the possible involvement of this water molecule as a substrate in the O-O bond formation. In addition, the PsbY subunit, which was absent in the 1.9 A structure of native PSII, was found in the Sr-PSII structure.

Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation.,Koua FH, Umena Y, Kawakami K, Shen JR Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3889-94. doi:, 10.1073/pnas.1219922110. Epub 2013 Feb 20. PMID:23426624[3]

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

See Also

References

  1. ↑ Shen JR, Ikeuchi M, Inoue Y. Stoichiometric association of extrinsic cytochrome c550 and 12 kDa protein with a highly purified oxygen-evolving photosystem II core complex from Synechococcus vulcanus. FEBS Lett. 1992 Apr 20;301(2):145-9. PMID:1314738
  2. ↑ Shen JR, Inoue Y. Binding and functional properties of two new extrinsic components, cytochrome c-550 and a 12-kDa protein, in cyanobacterial photosystem II. Biochemistry. 1993 Feb 23;32(7):1825-32. PMID:8382523
  3. ↑ Koua FH, Umena Y, Kawakami K, Shen JR. Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation. Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3889-94. doi:, 10.1073/pnas.1219922110. Epub 2013 Feb 20. PMID:23426624 doi:http://dx.doi.org/10.1073/pnas.1219922110

4il6, resolution 2.10Å

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