5ZZN image
Entry Detail
PDB ID:
5ZZN
Title:
Crystal structure of photosystem II from an SQDG-deficient mutant of Thermosynechococcus elongatus
Biological Source:
PDB Version:
Deposition Date:
2018-06-03
Release Date:
2018-08-01
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.19
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Photosystem II protein D1 1
Chain IDs:A, T (auth: a)
Chain Length:334
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II CP47 reaction center protein
Chain IDs:B, U (auth: b)
Chain Length:505
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II CP43 reaction center protein
Chain IDs:C, V (auth: c)
Chain Length:455
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II D2 protein
Chain IDs:D, W (auth: d)
Chain Length:342
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit alpha
Chain IDs:E, X (auth: e)
Chain Length:81
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Cytochrome b559 subunit beta
Chain IDs:F, Y (auth: f)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein H
Chain IDs:G (auth: H), Z (auth: h)
Chain Length:63
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein I
Chain IDs:H (auth: I), AA (auth: i)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein J
Chain IDs:I (auth: J), BA (auth: j)
Chain Length:40
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein K
Chain IDs:J (auth: K), CA (auth: k)
Chain Length:37
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein L
Chain IDs:K (auth: L), DA (auth: l)
Chain Length:36
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein M
Chain IDs:L (auth: M), EA (auth: m)
Chain Length:34
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Description:Photosystem II manganese-stabilizing polypeptide
Chain IDs:M (auth: O), FA (auth: o)
Chain Length:243
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein T
Chain IDs:N (auth: T), GA (auth: t)
Chain Length:30
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Description:Photosystem II 12 kDa extrinsic protein
Chain IDs:O (auth: U), HA (auth: u)
Chain Length:97
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Cytochrome c-550
Chain IDs:P (auth: V), IA (auth: v)
Chain Length:137
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center X protein
Chain IDs:R (auth: X), KA (auth: x)
Chain Length:39
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Ycf12
Chain IDs:Q (auth: Y), JA (auth: y)
Chain Length:29
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Polymer Type:polypeptide(L)
Description:Photosystem II reaction center protein Z
Chain IDs:S (auth: Z), LA (auth: z)
Chain Length:62
Number of Molecules:2
Biological Source:Thermosynechococcus elongatus (strain BP-1)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
FME H MET modified residue
HSK D HIS modified residue
Primary Citation
Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II inThermosynechococcus elongatus.
J. Biol. Chem. 293 14786 14797 (2018)
PMID: 30076221 DOI: 10.1074/jbc.RA118.004304

Abstact

Sulfoquinovosyl-diacylglycerol (SQDG) is one of the four lipids present in the thylakoid membranes. Depletion of SQDG causes different degrees of effects on photosynthetic growth and activities in different organisms. Four SQDG molecules bind to each monomer of photosystem II (PSII), but their role in PSII function has not been characterized in detail, and no PSII structure without SQDG has been reported. We analyzed the activities of PSII from an SQDG-deficient mutant of the cyanobacterium Thermosynechococcus elongatus by various spectroscopic methods, which showed that depletion of SQDG partially impaired the PSII activity by impairing secondary quinone (QB) exchange at the acceptor site. We further solved the crystal structure of the PSII dimer from the SQDG deletion mutant at 2.1 Å resolution and found that all of the four SQDG-binding sites were occupied by other lipids, most likely PG molecules. Replacement of SQDG at a site near the head of QB provides a possible explanation for the QB impairment. The replacement of two SQDGs located at the monomer-monomer interface by other lipids decreased the stability of the PSII dimer, resulting in an increase in the amount of PSII monomer in the mutant. The present results thus suggest that although SQDG binding in all of the PSII-binding sites is necessary to fully maintain the activity and stability of PSII, replacement of SQDG by other lipids can partially compensate for their functions.

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