PDBsum entry 3bz2

Electron transport

PDB id: 3bz2

Contents

Protein chains

335 a.a. *

490 a.a. *

447 a.a. *

340 a.a. *

82 a.a. *

35 a.a. *

65 a.a. *

35 a.a. *

34 a.a. *

37 a.a. *

37 a.a. *

34 a.a. *

243 a.a. *

32 a.a. *

97 a.a. *

137 a.a. *

28 a.a. *

37 a.a. *

28 a.a. *

62 a.a. *

Ligands

BCT

CLA ×35

PHO ×2

HEM ×2

PL9 ×3

OEC

BCR ×12

DGD ×7

LHG ×2

SQD ×5

LMG

LMT ×7

Metals

_CA

FE2

_CL

* Residue conservation analysis

Obsolete entry

PDB id:

3bz2

Name:

Electron transport

Title:

Crystal structure of cyanobacterial photosystem ii (part 2 of 2). This file contains second monomer of psii dimer

Structure:

Photosystem q(b) protein. Chain: a. Fragment: unp residues 1-344. Synonym: 32 kda thylakoid membrane protein, photosystem ii protein d1. Photosystem ii core light harvesting protein. Chain: b. Photosystem ii cp43 protein. Chain: c.

Source:

Thermosynechococcus elongatus. Organism_taxid: 197221. Strain: bp-1. Strain: bp-1

Resolution:

2.90Å R-factor: 0.249 R-free: 0.292

Authors:

A.Guskov,A.Gabdulkhakov,J.Kern,M.Broser,A.Zouni,W.Saenger

Key ref:

A.Guskov et al. (2009). Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride. Nat Struct Biol, 16, 334-342. PubMed id: 19219048 DOI: 10.1038/nsmb.1559

Date:

17-Jan-08 Release date: 20-Jan-09

Protein chain

P0A444  (PSBA1_THEEB) -  Photosystem II protein D1 1 from Thermosynechococcus elongatus (strain BP-1)

Seq: 360 a.a.

Struc: 335 a.a.

Protein chain

Q8DIQ1  (PSBB_THEEB) -  Photosystem II CP47 reaction center protein from Thermosynechococcus elongatus (strain BP-1)

Seq: 510 a.a.

Struc: 490 a.a.

Protein chain

Q8DIF8  (PSBC_THEEB) -  Photosystem II CP43 reaction center protein from Thermosynechococcus elongatus (strain BP-1)

Seq: 461 a.a.

Struc: 447 a.a.

Protein chain

Q8CM25  (PSBD_THEEB) -  Photosystem II D2 protein from Thermosynechococcus elongatus (strain BP-1)

Seq: 352 a.a.

Struc: 340 a.a.

Protein chain

Q8DIP0  (PSBE_THEEB) -  Cytochrome b559 subunit alpha from Thermosynechococcus elongatus (strain BP-1)

Seq: 84 a.a.

Struc: 82 a.a.

Protein chain

Q8DIN9  (PSBF_THEEB) -  Cytochrome b559 subunit beta from Thermosynechococcus elongatus (strain BP-1)

Seq: 45 a.a.

Struc: 35 a.a.

Protein chain

Q8DJ43  (PSBH_THEEB) -  Photosystem II reaction center protein H from Thermosynechococcus elongatus (strain BP-1)

Seq: 66 a.a.

Struc: 65 a.a.

Protein chain

Q8DJZ6  (PSBI_THEEB) -  Photosystem II reaction center protein I from Thermosynechococcus elongatus (strain BP-1)

Seq: 38 a.a.

Struc: 35 a.a.

Protein chain

P59087  (PSBJ_THEEB) -  Photosystem II reaction center protein J from Thermosynechococcus elongatus (strain BP-1)

Seq: 40 a.a.

Struc: 34 a.a.

Protein chain

Q9F1K9  (PSBK_THEEB) -  Photosystem II reaction center protein K from Thermosynechococcus elongatus (strain BP-1)

Seq: 46 a.a.

Struc: 37 a.a.

Protein chain

Q8DIN8  (PSBL_THEEB) -  Photosystem II reaction center protein L from Thermosynechococcus elongatus (strain BP-1)

Seq: 37 a.a.

Struc: 37 a.a.

Protein chain

Q8DHA7  (PSBM_THEEB) -  Photosystem II reaction center protein M from Thermosynechococcus elongatus (strain BP-1)

Seq: 36 a.a.

Struc: 34 a.a.

Protein chain

P0A431  (PSBO_THEEB) -  Photosystem II manganese-stabilizing polypeptide from Thermosynechococcus elongatus (strain BP-1)

Seq: 272 a.a.

Struc: 243 a.a.

Protein chain

Q8DIQ0  (PSBT_THEEB) -  Photosystem II reaction center protein T from Thermosynechococcus elongatus (strain BP-1)

Seq: 32 a.a.

Struc: 32 a.a.

Protein chain

Q9F1L5  (PSBU_THEEB) -  Photosystem II 12 kDa extrinsic protein from Thermosynechococcus elongatus (strain BP-1)

Seq: 134 a.a.

Struc: 97 a.a.

Protein chain

P0A386  (CY550_THEEB) -  Cytochrome c-550 from Thermosynechococcus elongatus (strain BP-1)

Seq: 163 a.a.

Struc: 137 a.a.

Protein chain

Q8DJI1  (YCF12_THEEB) -  Photosystem II reaction center protein Ycf12 from Thermosynechococcus elongatus (strain BP-1)

Seq: 46 a.a.

Struc: 28 a.a.

Protein chain

Q8DHE6  (Q8DHE6_SYNEL) -

Protein chain

No UniProt id for this chain

Struc: 28 a.a.

Protein chain

Q8DHJ2  (PSBZ_THEEB) -  Photosystem II reaction center protein Z from Thermosynechococcus elongatus (strain BP-1)

Seq: 62 a.a.

Struc: 62 a.a.

DOI no: 10.1038/nsmb.1559

Nat Struct Biol 16:334-342 (2009)

PubMed id: 19219048

Cyanobacterial photosystem II at 2.9-A resolution and the role of quinones, lipids, channels and chloride.

A.Guskov, J.Kern, A.Gabdulkhakov, M.Broser, A.Zouni, W.Saenger.

ABSTRACT

Photosystem II (PSII) is a large homodimeric protein-cofactor complex located in the photosynthetic thylakoid membrane that acts as light-driven water:plastoquinone oxidoreductase. The crystal structure of PSII from Thermosynechococcus elongatus at 2.9-A resolution allowed the unambiguous assignment of all 20 protein subunits and complete modeling of all 35 chlorophyll a molecules and 12 carotenoid molecules, 25 integral lipids and 1 chloride ion per monomer. The presence of a third plastoquinone Q(C) and a second plastoquinone-transfer channel, which were not observed before, suggests mechanisms for plastoquinol-plastoquinone exchange, and we calculated other possible water or dioxygen and proton channels. Putative oxygen positions obtained from a Xenon derivative indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII. The chloride position suggests a role in proton-transfer reactions because it is bound through a putative water molecule to the Mn(4)Ca cluster at a distance of 6.5 A and is close to two possible proton channels.

Selected figure(s)

Figure 3.
(a) Schematic view of the PQ-PQH[2] exchange cavity and the two entry and exit portals connecting the Q[B] and Q[C] sites to the PQ pool in the thylakoid membrane. Approximate dimensions are given in angstroms; Q[B] and Q[C] are colored cyan and yellow, respectively, the Q[B] site is highlighted in pink, and the three lipids forming the cork (the head groups for PG22, SQDG4 and MGDG18 are shown as red, green and white squares) nearly closing the cavity toward the cytoplasm are indicated. (b) Calculated channels (I and II, gray) for PQ-PQH[2] transfer between the PQ pool and the Q[B] and Q[C] sites, viewed from the cytoplasmic side. Shown are the PQs in the Q[B] site (light blue) and Q[C] site (yellow), non-heme Fe^2+ (blue sphere), Car15 (orange), Chl37 (green), SQDG4 (gray), cyt b-559 heme (dark blue) and the surrounding proteins (pink). Car[D2], Chl[D2] and MGDG7 are not shown. (c) Possible mechanisms for the PQ-PQH[2] exchange between the Q[B] site of PSII and the PQ pool in the thylakoid membrane, viewed from the cytoplasm. Channels I and II open toward the PQ pool. PQ is shown with a red and PQH[2] with a blue head group. The Q[B] site is highlighted pink, the Q[C] site in green and labeled; the yellow patch indicates a hydrophobic region formed by the fatty acids of MGDG7, MGDG18 and the phytol chain of Chl[D2]. Small arrows symbolize movements of PQ molecules. See text for explanations concerning the alternating, wriggling and single-channel mechanisms.

Figure 4.
(a) Position of Cl^- (green sphere) located in the native electron density (blue, contoured at 1.2 level) close to the Mn[4]Ca cluster (red and orange spheres; Mn1 is partially hidden behind Mn2). The coordinating amino acids are from D1 (yellow) except for D2-Lys317 (orange). (b) Enlarged view of the neighborhood of Cl^- showing coordinating amino acids and electron density (blue, contoured at 1.2 level) for a putative water molecule (purple sphere) located between Mn4 and Cl^-. Distances are given in angstroms.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 334-342) copyright 2009.

Figures were selected by an automated process.