PDBsum entry 5v2c

Electron transport, photosynthesis

PDB id: 5v2c

Contents

Protein chains

334 a.a.

504 a.a.

451 a.a.

342 a.a.

81 a.a.

34 a.a.

65 a.a.

38 a.a.

39 a.a.

37 a.a.

37 a.a.

34 a.a.

245 a.a.

30 a.a.

97 a.a.

137 a.a.

29 a.a.

40 a.a.

62 a.a.

32 a.a.

35 a.a.

Ligands

OEX ×2

BCT ×3

CLA ×70

PHO ×4

BCR ×22

PL9 ×4

SQD ×11

LMG ×14

GOL ×60

LMT ×18

LHG

PG4

PGE

P6G

EDO ×22

HTG ×24

1PE ×7

DGD ×10

HEM ×2

HEC ×2

2PE

PE8

Metals

FE2 ×2

_CL

_CA

_MG

Waters ×3789

PDB id:

5v2c

Name:

Electron transport, photosynthesis

Title:

Re-refinement of crystal structure of photosystem ii complex

Structure:

Photosystem ii protein d1. Chain: a, a. Synonym: psii d1 protein,photosystem ii q(b) protein. Photosystem ii cp47 reaction center protein. Chain: b, b. Synonym: psii 47 kda protein,protein cp-47. Photosystem ii cp43 reaction center protein. Chain: c, c. Synonym: psii 43 kda protein,protein cp-43.

Source:

Thermosynechococcus vulcanus. Organism_taxid: 32053. Organism_taxid: 32053

Resolution:

1.90Å R-factor: 0.095 R-free: 0.163

Authors:

J.Wang,J.M.Wiwczar,G.W.Brudvig

Key ref:

J.M.Wiwczar et al. (2017). Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria. Photosynth Res, 134, 175-182. PubMed id: 28741056

Date:

03-Mar-17 Release date: 30-Aug-17

Protein chains

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

Seq: 360 a.a.

Struc: 334 a.a.*

Protein chains

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

Seq: 505 a.a.

Struc: 504 a.a.

Protein chains

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

Seq: 451 a.a.

Struc: 451 a.a.

Protein chains

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

Seq: 342 a.a.

Struc: 342 a.a.*

Protein chains

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

Seq: 84 a.a.

Struc: 81 a.a.

Protein chain

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

Seq: 45 a.a.

Struc: 34 a.a.

Protein chains

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

Seq: 65 a.a.

Struc: 65 a.a.

Protein chains

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

Seq: 38 a.a.

Struc: 38 a.a.*

Protein chains

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

Seq: 40 a.a.

Struc: 39 a.a.*

Protein chains

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

Seq: 37 a.a.

Struc: 37 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 chain

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

Seq: 36 a.a.

Struc: 34 a.a.*

Protein chains

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

Seq: 244 a.a.

Struc: 245 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: 97 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

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

Seq: 30 a.a.

Struc: 29 a.a.

Protein chains

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

Seq: 40 a.a.

Struc: 40 a.a.

Protein chains

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

Seq: 62 a.a.

Struc: 62 a.a.

Protein chain

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

Seq: 45 a.a.

Struc: 32 a.a.

Protein chain

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

Seq: 36 a.a.

Struc: 35 a.a.*

* PDB and UniProt seqs differ at 12 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

Photosynth Res 134:175-182 (2017)

PubMed id: 28741056

Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria.

J.M.Wiwczar, A.M.LaFountain, J.Wang, H.A.Frank, G.W.Brudvig.

ABSTRACT

Photosystem II (PSII) of oxygenic photosynthetic organisms normally contains exclusively chlorophyll a (Chl a) as its major light-harvesting pigment. Chl a canonically consists of the chlorin headgroup with a 20-carbon, 4-isoprene unit, phytyl tail. We have examined the 1.9 Å crystal structure of PSII from thermophilic cyanobacteria reported by Shen and coworkers in 2012 (PDB accession of 3ARC/3WU2). A newly refined electron density map from this structure, presented here, reveals that some assignments of the cofactors may be different from those modeled in the 3ARC/3WU2 structure, including a specific Chl a that appears to have a truncated tail by one isoprene unit. We provide experimental evidence using high-performance liquid chromatography and mass spectrometry for a small population of Chl a esterified to a 15-carbon farnesyl tail in PSII of thermophilic cyanobacteria.