9PHW image
Deposition Date 2025-07-09
Release Date 2025-10-22
Last Version Date 2025-11-26
Entry Detail
PDB ID:
9PHW
Keywords:
Title:
Structure of the D1-Val185Asn mutated photosystem II complex with slow O-O bond formation reveals changes in the Cl1 water channel
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.99 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein D1 2
Gene (Uniprot):psbA2, psbA3
Mutagens:V185N
Chain IDs:A, V (auth: a)
Chain Length:344
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP47 reaction center protein
Gene (Uniprot):psbB
Chain IDs:B, W (auth: b)
Chain Length:507
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II CP43 reaction center protein
Gene (Uniprot):psbC
Chain IDs:C, X (auth: c)
Chain Length:460
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II D2 protein
Gene (Uniprot):psbD
Chain IDs:D, Y (auth: d)
Chain Length:352
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit alpha
Gene (Uniprot):psbE
Chain IDs:E, Z (auth: e)
Chain Length:81
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome b559 subunit beta
Gene (Uniprot):psbF
Chain IDs:F, AA (auth: f)
Chain Length:44
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein H
Gene (Uniprot):psbH
Chain IDs:G (auth: H), BA (auth: h)
Chain Length:64
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein I
Gene (Uniprot):psbI
Chain IDs:H (auth: I), CA (auth: i)
Chain Length:38
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein J
Gene (Uniprot):psbJ
Chain IDs:I (auth: J), DA (auth: j)
Chain Length:35
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein K
Gene (Uniprot):psbK
Chain IDs:J (auth: K), EA (auth: k)
Chain Length:45
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein L
Gene (Uniprot):psbL
Chain IDs:K (auth: L), FA (auth: l)
Chain Length:39
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein M
Gene (Uniprot):psbM
Chain IDs:L (auth: M), GA (auth: m)
Chain Length:35
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II manganese-stabilizing polypeptide
Gene (Uniprot):psbO
Chain IDs:M (auth: O), HA (auth: o)
Chain Length:274
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Sll1638 protein
Gene (Uniprot):psbQ
Chain IDs:N (auth: Q), IA (auth: q)
Chain Length:149
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II protein Y
Gene (Uniprot):psbY
Chain IDs:O (auth: R), JA (auth: r)
Chain Length:39
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein T
Gene (Uniprot):psbT
Chain IDs:P (auth: T), KA (auth: t)
Chain Length:31
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II 12 kDa extrinsic protein
Gene (Uniprot):psbU
Chain IDs:Q (auth: U), LA (auth: u)
Chain Length:131
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cytochrome c-550
Gene (Uniprot):psbV
Chain IDs:R (auth: V), MA (auth: v)
Chain Length:160
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center X protein
Gene (Uniprot):psbX
Chain IDs:S (auth: X), NA (auth: x)
Chain Length:39
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Ycf12
Gene (Uniprot):psb30
Chain IDs:T (auth: Y), OA (auth: y)
Chain Length:39
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photosystem II reaction center protein Z
Gene (Uniprot):psbZ
Chain IDs:U (auth: Z), PA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Synechocystis sp. PCC 6803
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET modified residue
Primary Citation
Structure of the D1-Val185Asn mutated photosystem II complex with slow O-O bond formation reveals changes in the Cl1 water channel.
Proc.Natl.Acad.Sci.USA 122 e2522652122 e2522652122 (2025)
PMID: 41237214 DOI: 10.1073/pnas.2522652122

Abstact

During photosynthesis, the photosystem II (PSII) enzyme catalyzes the light-driven oxidation of water, fueling life on Earth by storing light energy and releasing O2 as a byproduct. Determining the molecular mechanism for this water oxidation reaction has been of significant interest for the development of synthetic catalysts, but many details remain elusive. One of the open questions is how protons are strategically removed from the active site, a Mn4CaO5 cluster called the oxygen-evolving complex (OEC), during the reaction cycle via conserved water channels, and how proton transfer contributes to O-O bond formation energetics. Site-directed mutagenesis studies have investigated the role of conserved amino acid side chains in facilitating proton transfer. One of the most influential mutations is the Val185Asn substitution on the D1 subunit, which substantially slows O2 release kinetics without abolishing catalytic activity. Forming a molecular understanding of how this mutation affects the active site will provide insight into the water oxidation reaction mechanism. Here, we investigated the structural basis of the Val185Asn substitution by determining a 1.99 Å-resolution cryo-EM structure. We observed that Asn185 orients away from the OEC and donates a H-bond to Cl1, a conserved chloride ion. We furthermore observed an alternative D2-Glu312-facing conformation of the D2-Lys317 side chain in the Cl1 water channel, a conformation that is consistent with recent models for proton transfer. These changes also produce perturbations to the hydrogen-bonding network. Overall, these finding provide insight into proton transfer in the Cl1 channel and its effect on the water oxidation reaction mechanism.

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