PDBsum entry 2uxm

Photosynthesis

PDB id: 2uxm

Contents

Protein chains

241 a.a. *

281 a.a. *

303 a.a. *

Ligands

GOL ×4

BCL ×4

LDA ×9

BPH ×2

UQ2

PO4

HTO

U10

SPO

Metals

_FE

Waters ×241

* Residue conservation analysis

PDB id:

2uxm

Name:

Photosynthesis

Title:

X-ray high resolution structure of the photosynthetic reaction center from rb. Sphaeroides at ph 10 in the charge-separated state, 2nd dataset

Structure:

Reaction center protein h chain. Chain: h. Synonym: photosynthetic reaction center h subunit. Other_details: ph 10 charge-separated state. Reaction center protein l chain. Chain: l. Synonym: photosynthetic reaction center l subunit. Other_details: ph 10 charge-separated state. Reaction center protein m chain.

Source:

Rhodobacter sphaeroides. Organism_taxid: 1063. Organism_taxid: 1063

Resolution:

2.70Å R-factor: 0.187 R-free: 0.221

Authors:

J.Koepke,R.Diehm,G.Fritzsch

Key ref:

J.Koepke et al. (2007). pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J Mol Biol, 371, 396-409. PubMed id: 17570397 DOI: 10.1016/j.jmb.2007.04.082

Date:

28-Mar-07 Release date: 03-Jul-07

Protein chain

P0C0Y7  (RCEH_CERSP) -  Reaction center protein H chain from Cereibacter sphaeroides

Seq: 260 a.a.

Struc: 241 a.a.

Protein chain

P0C0Y8  (RCEL_CERSP) -  Reaction center protein L chain from Cereibacter sphaeroides

Seq: 282 a.a.

Struc: 281 a.a.

Protein chain

P0C0Y9  (RCEM_CERSP) -  Reaction center protein M chain from Cereibacter sphaeroides

Seq: 308 a.a.

Struc: 303 a.a.

DOI no: 10.1016/j.jmb.2007.04.082

J Mol Biol 371:396-409 (2007)

PubMed id: 17570397

pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states.

J.Koepke, E.M.Krammer, A.R.Klingen, P.Sebban, G.M.Ullmann, G.Fritzsch.

ABSTRACT

The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolution of 1.87 A, which is the best ever reported for the bacterial reaction center protein. Our crystallographic data confirm the existence of two different binding positions of the secondary quinone (QB). We observe a new orientation of QB in its distal position, which shows no ring-flip compared to the orientation in the proximal position. Datasets collected for the different pH values show a pH-dependence of the population of the proximal position. The new orientation of QB in the distal position and the pH-dependence could be confirmed by continuum electrostatics calculations. Our calculations are in agreement with the experimentally observed proton uptake upon charge separation. The high resolution of our crystallographic data allows us to identify new water molecules and external residues being involved in two previously described hydrogen bond proton channels. These extended proton-transfer pathways, ending at either of the two oxo-groups of QB in its proximal position, provide additional evidence that ring-flipping is not required for complete protonation of QB upon reduction.

Selected figure(s)

Figure 2.
Figure 2. (a) Electron density around the distal and proximal Q_B positions in the structure of this work (pH 8, dark-adapted state; PDB entry 2j8c). The 0.2 and the 1σ levels of the density are depicted in blue and magenta wireframes, respectively. The models for the distal (orange) and the proximal (yellow) positions are shown as stick model. The two head-groups are tilted out of the image plane by about ±15°.
(b) Superposition of the two Q_B positions, color-coded in yellow, orange, and red, respectively, with the structures from Stowell et al. (PDB entries 1aig and 1aij) of the same state and at the same pH, shown in red. Hydrogen bonds to neighboring protein atoms are indicated by broken green lines, with their length given in Å.
(c) Schematic drawing of the Q_B movement. Distal position in black, hypothetical intermediate position in green, and proximal Q_B position in blue. Hydrogen bonds to the distal position are color-coded orange, to the intermediate position in red, and to the proximal Q_B position in magenta. The length of the total Q_B movement and the C^α–C^α distance are indicated by arrows.

Figure 6.
Figure 6. Proton-uptake upon reduction of Q[B] as calculated using the program GMCT. The total proton-uptake is shown by a continuous line and experimental values (taken from Tandori et al.^22) by black crosses with error bars. The contribution of Asp L213 (broken line) and the protonation of the semiquinone (dotted line) are shown additionally. The dash-dot line describes the proton uptake by the rest of the protein.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 396-409) copyright 2007.

Figures were selected by the author.