PDBsum entry 5h2f

Photosynthesis

PDB id: 5h2f

Contents

Protein chains

334 a.a.

505 a.a.

451 a.a.

342 a.a.

79 a.a.

33 a.a.

63 a.a.

35 a.a.

36 a.a.

37 a.a.

35 a.a.

243 a.a.

30 a.a.

97 a.a.

137 a.a.

29 a.a.

37 a.a.

62 a.a.

31 a.a.

36 a.a.

40 a.a.

36 a.a.

Ligands

OEX ×2

CLA ×70

PHO ×4

BCR ×18

LMG ×12

PL9 ×4

LHG ×12

SQD ×8

LMT ×11

UNL ×27

DMS

BCT

HTG

DGD

HEM ×2

RRX ×2

HEC ×2

Metals

_MG

FE2 ×2

_CL

_CA

Waters ×2370

PDB id:

5h2f

Name:

Photosynthesis

Title:

Crystal structure of the psbm-deletion mutant of photosystem ii

Structure:

Photosystem ii protein d1 1. Chain: a, a. Fragment: unp residues 11-344. Synonym: psii d1 protein 1,photosystem ii q(b) protein 1. Photosystem ii cp47 reaction center protein. Chain: b, b. Fragment: unp residues 2-506. Synonym: psii 47 kda protein,protein cp-47. Photosystem ii cp43 reaction center protein.

Source:

Thermosynechococcus elongatus (strain bp-1). Organism_taxid: 197221. Strain: bp-1. Thermosynechococcus elongatus. Strain: bp-1

Resolution:

2.20Å R-factor: 0.177 R-free: 0.226

Authors:

S.Uto,K.Kawakami,Y.Umena,M.Iwai,M.Ikeuchi,J.R.Shen,N.Kamiya

Key ref:

S.Uto et al. (2017). Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II. Faraday Discuss, 198, 107-120. PubMed id: 28272640 DOI: 10.1039/c6fd00213g

Date:

15-Oct-16 Release date: 22-Mar-17

Protein chains

P0A444  (PSBA1_THEEB) -  Photosystem II protein D1 1 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 360 a.a.

Struc: 334 a.a.

Protein chains

Q8DIQ1  (PSBB_THEEB) -  Photosystem II CP47 reaction center protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 510 a.a.

Struc: 505 a.a.

Protein chains

Q8DIF8  (PSBC_THEEB) -  Photosystem II CP43 reaction center protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 461 a.a.

Struc: 451 a.a.

Protein chains

Q8CM25  (PSBD_THEEB) -  Photosystem II D2 protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 352 a.a.

Struc: 342 a.a.

Protein chains

Q8DIP0  (PSBE_THEEB) -  Cytochrome b559 subunit alpha from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 84 a.a.

Struc: 79 a.a.

Protein chain

Q8DIN9  (PSBF_THEEB) -  Cytochrome b559 subunit beta from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 45 a.a.

Struc: 33 a.a.

Protein chains

Q8DJ43  (PSBH_THEEB) -  Photosystem II reaction center protein H from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 66 a.a.

Struc: 63 a.a.

Protein chain

Q8DJZ6  (PSBI_THEEB) -  Photosystem II reaction center protein I from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 38 a.a.

Struc: 35 a.a.*

Protein chain

P59087  (PSBJ_THEEB) -  Photosystem II reaction center protein J from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 40 a.a.

Struc: 36 a.a.

Protein chains

Q9F1K9  (PSBK_THEEB) -  Photosystem II reaction center protein K from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 46 a.a.

Struc: 37 a.a.

Protein chains

Q8DIN8  (PSBL_THEEB) -  Photosystem II reaction center protein L from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 37 a.a.

Struc: 35 a.a.

Protein chains

P0A431  (PSBO_THEEB) -  Photosystem II extrinsic protein O from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 272 a.a.

Struc: 243 a.a.

Protein chains

Q8DIQ0  (PSBT_THEEB) -  Photosystem II reaction center protein T from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 32 a.a.

Struc: 30 a.a.*

Protein chains

Q9F1L5  (PSBU_THEEB) -  Photosystem II extrinsic protein U from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 134 a.a.

Struc: 97 a.a.

Protein chains

P0A386  (CY550_THEEB) -  Photosystem II extrinsic protein V from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 163 a.a.

Struc: 137 a.a.

Protein chains

Q8DJI1  (YCF12_THEEB) -  Photosystem II reaction center protein Psb30 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 46 a.a.

Struc: 29 a.a.

Protein chain

Q9F1R6  (PSBX_THEEB) -  Photosystem II reaction center protein X from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 41 a.a.

Struc: 37 a.a.

Protein chains

Q8DHJ2  (PSBZ_THEEB) -  Photosystem II reaction center protein Z from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 62 a.a.

Struc: 62 a.a.

Protein chain

Q8DIN9  (PSBF_THEEB) -  Cytochrome b559 subunit beta from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 45 a.a.

Struc: 31 a.a.

Protein chain

Q8DJZ6  (PSBI_THEEB) -  Photosystem II reaction center protein I from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 38 a.a.

Struc: 36 a.a.*

Protein chain

P59087  (PSBJ_THEEB) -  Photosystem II reaction center protein J from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 40 a.a.

Struc: 40 a.a.

Protein chain

Q9F1R6  (PSBX_THEEB) -  Photosystem II reaction center protein X from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)

Seq: 41 a.a.

Struc: 36 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

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: 10.1039/c6fd00213g

Faraday Discuss 198:107-120 (2017)

PubMed id: 28272640

Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II.

S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya.

ABSTRACT

Photosystem II (PSII) is a membrane protein complex that performs light-induced electron transfer and oxygen evolution from water. PSII consists of 19 or 20 subunits in its crystal form and binds various cofactors such as chlorophyll a, plastoquinone, carotenoid, and lipids. After initial light excitation, the charge separation produces an electron, which is transferred to a plastoquinone molecule (Q_A) and then to another plastoquinone (Q_B). PsbM is a low-molecular-weight subunit with one transmembrane helix, and is located in the monomer-monomer interface of the PSII dimer. The function of PsbM has been reported to be stabilization of the PSII dimer and maintenance of electron transfer efficiency of PSII based on previous X-ray crystal structure analysis at a resolution of 4.2 Å. In order to elucidate the structure-function relationships of PsbM in detail, we improved the quality of PSII crystals from a PsbM-deleted mutant (ΔPsbM-PSII) of Thermosynechococcus elongatus, and succeeded in improving the diffraction quality to a resolution of 2.2 Å. X-ray crystal structure analysis of ΔPsbM-PSII showed that electron densities for the PsbM subunit and neighboring carotenoid and detergent molecules were absent in the monomer-monomer interface. The overall structure of ΔPsbM-PSII was similar to wild-type PSII, but the arrangement of the hydrophobic transmembrane subunits was significantly changed by the deletion of PsbM, resulting in a slight widening of the lipid hole involving Q_B. The lipid hole-widening further induced structural changes of the bicarbonate ion coordinated to the non-heme Fe(ii) atom and destabilized the polypeptide chains around the Q_Bbinding site located far from the position of PsbM. The fluorescence decay measurement indicated that the electron transfer rate from Q_Ato Q_Bwas decreased in ΔPsbM-PSII compared with wild-type PSII. The functional change in electron transfer efficiency was fully interpreted based on structural changes caused by the deletion of the PsbM subunit.