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- PDB-8tow: Structure of a mutated photosystem II complex reveals perturbatio... -

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Basic information

Entry
Database: PDB / ID: 8tow
TitleStructure of a mutated photosystem II complex reveals perturbation of the oxygen-evolving complex
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
  • Sll1638 protein
KeywordsPHOTOSYNTHESIS / photosystem II / oxygen-evolving complex / D1-D170E / S1 state / transition metals / metalloenzyme
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide ...plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding / identical protein binding
Similarity search - Function
Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor ...Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Photosystem II CP47 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein M / CyanoQ / Photosystem II reaction center protein J / Photosystem II reaction center protein Z / Photosystem II reaction center protein Y / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II extrinsic protein V / Photosystem II extrinsic protein U / Photosystem II reaction center protein L / Photosystem II reaction center protein Psb30
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsFlesher, D.A. / Liu, J. / Wang, J. / Gisriel, C.J. / Yang, K.R. / Batista, V.S. / Debus, R.J. / Brudvig, G.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: J Biol Chem / Year: 2024
Title: Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels.
Authors: David A Flesher / Jinchan Liu / Jimin Wang / Christopher J Gisriel / Ke R Yang / Victor S Batista / Richard J Debus / Gary W Brudvig /
Abstract: Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at ...Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a MnCaO cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the MnCaO cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.
History
DepositionAug 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 2.0Jul 3, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / em_admin / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 2.1Jul 24, 2024Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 2.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1 2
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
Q: Sll1638 protein
R: Photosystem II protein Y
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
X: Photosystem II reaction center X protein
Y: Photosystem II reaction center protein Ycf12
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1 2
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
q: Sll1638 protein
r: Photosystem II protein Y
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
x: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Ycf12
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)816,784274
Polymers660,68042
Non-polymers156,104232
Water22,8791270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoRrTtUuXx...

#1: Protein Photosystem II protein D1 2


Mass: 39758.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P16033
#2: Protein Photosystem II CP47 reaction center protein


Mass: 55954.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P05429
#3: Protein Photosystem II CP43 reaction center protein


Mass: 50344.723 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P09193
#4: Protein Photosystem II D2 protein


Mass: 39519.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P09192
#7: Protein Photosystem II reaction center protein H


Mass: 7120.404 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P14835
#8: Protein/peptide Photosystem II reaction center protein I


Mass: 4338.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q54697
#9: Protein/peptide Photosystem II reaction center protein J


Mass: 3976.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73070
#10: Protein/peptide Photosystem II reaction center protein K


Mass: 5114.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P15819
#11: Protein/peptide Photosystem II reaction center protein L


Mass: 4476.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55354
#12: Protein/peptide Photosystem II reaction center protein M


Mass: 3910.639 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72701
#13: Protein Photosystem II manganese-stabilizing polypeptide


Mass: 29939.584 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P10549
#15: Protein/peptide Photosystem II protein Y


Mass: 4204.958 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73676
#16: Protein/peptide Photosystem II reaction center protein T


Mass: 3571.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74787
#17: Protein Photosystem II 12 kDa extrinsic protein


Mass: 14256.163 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55332
#19: Protein/peptide Photosystem II reaction center X protein


Mass: 4189.036 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72575
#20: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 4143.993 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55438
#21: Protein Photosystem II reaction center protein Z


Mass: 6736.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73528

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha


Mass: 9454.577 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P09190
#6: Protein/peptide Cytochrome b559 subunit beta


Mass: 4935.784 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P09191

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Protein , 2 types, 4 molecules QqVv

#14: Protein Sll1638 protein


Mass: 16494.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73048
#18: Protein Cytochrome c-550


Mass: 17901.045 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55013

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Sugars , 2 types, 72 molecules

#31: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#34: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 15 types, 1430 molecules

#22: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#24: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#27: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#29: Chemical
ChemComp-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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#30: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C41H78O12S
#32: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#33: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#35: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#36: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#37: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1270 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: photosystem II / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129229 / Symmetry type: POINT

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