Surprises and pitfalls arising from (pseudo)symmetry

Zwart, Peter H.; Grosse‐Kunstleve, Ralf W.; Лебедев, А. А.; Murshudov, Garib N.; Adams, Paul D.

doi:10.1107/s090744490705531x

Cited by 97 publications

(115 citation statements)

References 67 publications

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“…Our final refined model contained two nearly identical molecules in the asymmetric unit at positions (x, y, z) and (x + 1/2, y, z), with the (x + 1/2, y, z) molecule demonstrating rotational disorder (PDB entry 3ks1; Robbins et al, 2010). Zwart et al (2008) described a crystallographic scenario that can occur when such an observation is made. In the monoclinic P2 1 case with a pseudo-translational operator (x + 1/2, y, z), the unit cell consists of four molecules [A (x, y, z), B (x + 1/2, y, z), C (Àx + 1/2, y + 1/2, Àz) and D (Àx, y + 1/2, Àz)].…”

Section: Introductionmentioning

confidence: 99%

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP2₁with a doubledaaxis

Robbins

Domsic

Agbandje‐McKenna

et al. 2010

Acta Crystallogr D Biol Cryst

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PDB Reference: human carbonic anhydrase II, 3mwo.The crystal structure of human carbonic anhydrase II in the monoclinic P2 1 space group with a doubled a axis from that of the usually observed unit cell has recently been reported, with one of the two molecules in the asymmetric unit demonstrating rotational disorder [Robbins et al. (2010), Acta Cryst. D66, 628-634]. The structure has been redetermined, with the coordinates of both pseudosymmetrically related molecules in the crystallographic asymmetric unit translated by x 0 = x AE 1/4, and no rotational disorder is observed. This corresponds to a different choice of how the four molecules in the unit cell should be grouped into pairs that represent a single asymmetric unit.

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Section: Introductionmentioning

confidence: 99%

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP2₁with a doubledaaxis

Robbins

Domsic

Agbandje‐McKenna

et al. 2010

Acta Crystallogr D Biol Cryst

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“…Data were reduced by using HKL2000 (25) and TRUNCATE (26). Analysis of the data with phenix.xtriage from the PHENIX suite (27) revealed that the crystal was merohedrally twinned. As the crystal was found to be isomorphous to those described previously (24), direct refinement of the existing model (PDB accession code 3FSN) against the higher resolution dataset was performed with REFMAC5 (28).…”

Section: Purification Of Cross-linked Products and Identification Ofmentioning

confidence: 99%

Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity

Golczak

Kiser

Lodowski

et al. 2010

Journal of Biological Chemistry

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Regeneration of visual chromophore in the vertebrate visual cycle involves the retinal pigment epithelium-specific protein RPE65, the key enzyme catalyzing the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol. Although RPE65 has no predicted membrane spanning domains, this protein predominantly associates with microsomal fractions isolated from bovine retinal pigment epithelium (RPE). We have re-examined the nature of RPE65 interactions with native microsomal membranes by using extraction and phase separation experiments. We observe that hydrophobic interactions are the dominant forces that promote RPE65 association with these membranes. These results are consistent with the crystallographic model of RPE65, which features a large lipophilic surface that surrounds the entrance to the catalytic site of this enzyme and likely interacts with the hydrophobic core of the endoplasmic reticulum membrane. Moreover, we report a critical role for phospholipid membranes in preserving the retinoid isomerization activity and physical properties of RPE65. Isomerase activity measured in bovine RPE was highly sensitive to phospholipase A 2 treatment, but the observed decline in 11-cis-retinol production did not directly reflect inhibition by products of lipid hydrolysis. Instead, a direct correlation between the kinetics of phospholipid hydrolysis and retinoid isomerization suggests that the lipid membrane structure is critical for RPE65 enzymatic activity. We also provide evidence that RPE65 operates in a multiprotein complex with retinol dehydrogenase 5 and retinal G protein-coupled receptor in RPE microsomes. Modifications in the phospholipid environment affecting interactions with these protein components may be responsible for the alterations in retinoid metabolism observed in phospholipid-depleted RPE microsomes. Thus, our results indicate that the enzymatic activity of native RPE65 strongly depends on its membrane binding and phospholipid environment.In vertebrates, the perception of light is preceded by a quantum event in which a photon of light hits the 11-cis-retinylidene chromophore of rhodopsin in the retina. Photoisomerization of this chromophore to its all-trans isomer results in activation of rhodopsin triggering a cascade of signal transduction events (summarized in Ref. 1). This process simultaneously leads to loss of photoreceptor light sensitivity making continuous regeneration of 11-cis-retinal a requirement to sustain vision. The visual (retinoid) cycle is the fundamental series of reactions responsible for regeneration of the visual chromophore that occurs in photoreceptors and the retinal pigment epithelium (RPE) 4 (summarized in Ref.2). The key component of this enzymatic cycle is the RPE-specific microsomal membrane protein known as RPE65 (3-5). The importance of RPE65 in the retinoid cycle is underscored by the metabolic dysfunction found in Rpe65 Ϫ/Ϫ mice, which is characterized by complete lack of 11-cis-retinoid production accompanied by accumulation of the all-tr...

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“…Crystals of RPE65 obtained in the presence of racemic emixustat belonged to space group P6 5 22 with 1 monomer in the asymmetric unit, whereas crystals containing (R)-or (S)-emixustat or MB-002 belonged to space group P6 5 with 2 monomers in the asymmetric unit. The absence of twinning was determined with phenix.xtraige (59).…”

Section: 0mentioning

confidence: 99%

Molecular pharmacodynamics of emixustat in protection against retinal degeneration

Zhang

Kiser²,

Badiee

et al. 2015

J. Clin. Invest.

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Surprises and pitfalls arising from (pseudo)symmetry

Abstract: The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.

Cited by 97 publications

References 67 publications

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP2₁with a doubledaaxis

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP2₁with a doubledaaxis

Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity

Molecular pharmacodynamics of emixustat in protection against retinal degeneration

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Surprises and pitfalls arising from (pseudo)symmetry

Abstract: The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented.

Cited by 97 publications

References 67 publications

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP21with a doubledaaxis

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP21with a doubledaaxis

Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity

Molecular pharmacodynamics of emixustat in protection against retinal degeneration

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Product

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Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP2₁with a doubledaaxis

Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinicP2₁with a doubledaaxis