PDBsum entry 3a0b

Electron transport

PDB id: 3a0b

Contents

Protein chains

335 a.a. *

485 a.a. *

447 a.a. *

340 a.a. *

82 a.a. *

35 a.a. *

64 a.a. *

35 a.a. *

34 a.a. *

36 a.a. *

37 a.a. *

36 a.a. *

242 a.a. *

30 a.a. *

98 a.a. *

137 a.a. *

34 a.a. *

28 a.a. *

24 a.a. *

62 a.a. *

Ligands

OEC ×2

CLA ×70

PHO ×4

PQ9 ×4

BCR ×22

LHG ×2

MGE ×8

DGD ×8

HEM ×4

Metals

_BR ×4

FE2 ×2

* Residue conservation analysis

PDB id:

3a0b

Name:

Electron transport

Title:

Crystal structure of br-substituted photosystem ii complex

Structure:

Photosystem q(b) protein. Chain: a, a. Synonym: 32 kda thylakoid membrane protein, photosystem ii protein d1. Photosystem ii core light harvesting protein. Chain: b, b. Photosystem ii cp43 protein. Chain: c, c. Photosystem ii d2 protein.

Source:

Thermosynechococcus vulcanus. Synechococcus vulcanus. Organism_taxid: 32053. Cellular_location: thylakoid membrane. Cellular_location: thylakoid membrane

Resolution:

3.70Å R-factor: 0.302 R-free: 0.358

Authors:

K.Kawakami,Y.Umena,N.Kamiya,J.-R.Shen

Key ref:

K.Kawakami et al. (2009). Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography. Proc Natl Acad Sci U S A, 106, 8567-8572. PubMed id: 19433803 DOI: 10.1073/pnas.0812797106

Date:

16-Mar-09 Release date: 19-May-09

Protein chains

P51765  (PSBA_THEVL) -  Photosystem II protein D1 from Thermostichus vulcanus

Seq: 360 a.a.

Struc: 335 a.a.

Protein chains

D0VWR1  (PSBB_THEVL) -  Photosystem II CP47 reaction center protein (Fragment) from Thermostichus vulcanus

Seq: 505 a.a.

Struc: 485 a.a.

Protein chains

D0VWR7  (PSBC_THEVL) -  Photosystem II CP43 reaction center protein (Fragment) from Thermostichus vulcanus

Seq: 451 a.a.

Struc: 447 a.a.

Protein chains

D0VWR8  (PSBD_THEVL) -  Photosystem II D2 protein (Fragment) from Thermostichus vulcanus

Seq: 342 a.a.

Struc: 340 a.a.

Protein chains

P12238  (PSBE_THEVL) -  Cytochrome b559 subunit alpha from Thermostichus vulcanus

Seq: 84 a.a.

Struc: 82 a.a.

Protein chains

P12239  (PSBF_THEVL) -  Cytochrome b559 subunit beta from Thermostichus vulcanus

Seq: 45 a.a.

Struc: 35 a.a.

Protein chains

P19052  (PSBH_THEVL) -  Photosystem II reaction center protein H (Fragment) from Thermostichus vulcanus

Seq: 65 a.a.

Struc: 64 a.a.

Protein chains

P12240  (PSBI_THEVL) -  Photosystem II reaction center protein I from Thermostichus vulcanus

Seq: 38 a.a.

Struc: 35 a.a.

Protein chains

Q7DGD4  (PSBJ_THEVL) -  Photosystem II reaction center protein J from Thermostichus vulcanus

Seq: 40 a.a.

Struc: 34 a.a.

Protein chains

P19054  (PSBK_THEVL) -  Photosystem II reaction center protein K (Fragment) from Thermostichus vulcanus

Seq: 37 a.a.

Struc: 36 a.a.

Protein chains

P12241  (PSBL_THEVL) -  Photosystem II reaction center protein L from Thermostichus vulcanus

Seq: 37 a.a.

Struc: 37 a.a.

Protein chains

P12312  (PSBM_THEVL) -  Photosystem II reaction center protein M from Thermostichus vulcanus

Seq: 36 a.a.

Struc: 36 a.a.

Protein chains

D0VWR2  (PSBO_THEVL) -  Photosystem II extrinsic protein O from Thermostichus vulcanus

Seq: 244 a.a.

Struc: 242 a.a.

Protein chains

P12313  (PSBT_THEVL) -  Photosystem II reaction center protein T from Thermostichus vulcanus

Seq: 32 a.a.

Struc: 30 a.a.

Protein chains

P56152  (PSBU_THEVL) -  Photosystem II extrinsic protein U from Thermostichus vulcanus

Seq: 104 a.a.

Struc: 98 a.a.

Protein chains

P0A387  (CY550_THEVL) -  Photosystem II extrinsic protein V from Thermostichus vulcanus

Seq: 163 a.a.

Struc: 137 a.a.

Protein chains

D0VWR4  (PSBX_THEVL) -  Photosystem II reaction center protein X (Fragment) from Thermostichus vulcanus

Seq: 40 a.a.

Struc: 34 a.a.

Protein chains

D0VWR3  (PSB30_THEVL) -  Photosystem II reaction center protein Psb30 (Fragment) from Thermostichus vulcanus

Seq: 30 a.a.

Struc: 28 a.a.

Protein chains

No UniProt id for this chain

Struc: 24 a.a.

Protein chains

D0VWR5  (PSBZ_THEVL) -  Photosystem II reaction center protein Z from Thermostichus vulcanus

Seq: 62 a.a.

Struc: 62 a.a.

Enzyme reactions

• Enzyme class: Chains A, D, a, d: E.C.1.10.3.9 - photosystem Ii.
• Reaction: 2 a plastoquinone + 4 hnu + 2 H2O = 2 a plastoquinol + O2

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1073/pnas.0812797106

Proc Natl Acad Sci U S A 106:8567-8572 (2009)

PubMed id: 19433803

Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography.

K.Kawakami, Y.Umena, N.Kamiya, J.R.Shen.

ABSTRACT

The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions. Substitution of Cl(-) with Br(-) did not inhibit oxygen evolution, whereas substitution of Cl(-) with I(-) completely inhibited oxygen evolution, indicating the efficient replacement of Cl(-) by I(-). PSII with Br(-) and I(-)substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn(4)Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn(4)Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl(-) anions are required to maintain the coordination structure of the Mn(4)Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.

Selected figure(s)

Figure 3.
Location of the 2 anion-binding sites in PSII. (A) Composite omit Fo-Fc map (blue) and anomalous map (red) of PSII with Br^− substitution contoured at σ = 1.0 and 4.0, respectively, superimposed on the structure of the Mn[4]Ca cluster and its surrounding regions. The structure of PSII with Br^−substitution was shown by the molecular replacement method with the structure of the PDB code 2AXT as the search model. Color codes for the residues are as follows: yellow, D1; green, D2; orange, CP43; purple, Mn atoms. (B) Composite omit Fo-Fc map (blue) and anomalous map (red) of I^−-substituted PSII contoured at σ = 1.0 and 4.0, respectively, superimposed on the structure of the Mn[4]Ca cluster and its surrounding regions. The structure of PSII with I^− substitution was shown by the molecular replacement method. The color codes for the residues are the same as in A. (C) Location of Br[1] relative to the proton exit channel proposed in (16, 27–29). The residues of PsbO are drawn in blue, and the residues of other subunits are in the same colors as in A. The directions of atoms from Cα to Cβ in the residues are indicated by capsule-shaped objects.

Figure 4.
Additional binding sites of I^− in I^−-substituted PSII. (A) Fo-Fc omit map of PSII with I^− substitution (red) contoured at σ = 3.0, superimposed on the structure of CP47 (green) obtained by the molecular replacement method, showing the association of I^− with CP47-Cys-112. (B) Fo-Fc omit map of PSII with I^− substitution (red) contoured at σ = 3.0, superimposed on the structure of PsbTc (pink), showing the association of I^− with PsbTc-Cys-12. The capsule-shaped objects show the direction of atoms from Cα to Cβ in the 2 Cys residues. (C) 2Fo-Fc map (blue, σ = 1.0) and omit Fo-Fc map (red, σ = 2.0) of PSII with I^− substitution around the region of D2-Tyr-160(Y[D]), together with the structure of D2 (green) in this region.

Figures were selected by an automated process.