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Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form.

Shevchenko V, Gushchin I, Polovinkin V, Round E, Borshchevskiy V, Utrobin P, Popov A, Balandin T, Büldt G, Gordeliy V - PLoS ONE (2014)

Bottom Line: The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins.The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface.All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

View Article: PubMed Central - PubMed

Affiliation: Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany; Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia.

ABSTRACT
Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

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Related in: MedlinePlus

Structure of the HmBRI trimer and its D-E loop.(A) Comparison of the HmBRI trimer structure (green) with that of HsBR [23] (yellow). HmBRI trimer aligns well in the extracellular region, but the protomers are slightly rotated at the cytoplasmic side. (B) Magnification of the D-E loop. Unlike in other trimerizing retinylidene proteins, in HmBRI the loop is extended and makes contact to the adjacent protomer. (C) Wall-eyed stereogram of the HmBRI D-E loop. The adjacent protomer is shown in orange and its residues are marked by a prime. Three structural water molecules are observed that stabilize the loop structure.
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pone-0112873-g007: Structure of the HmBRI trimer and its D-E loop.(A) Comparison of the HmBRI trimer structure (green) with that of HsBR [23] (yellow). HmBRI trimer aligns well in the extracellular region, but the protomers are slightly rotated at the cytoplasmic side. (B) Magnification of the D-E loop. Unlike in other trimerizing retinylidene proteins, in HmBRI the loop is extended and makes contact to the adjacent protomer. (C) Wall-eyed stereogram of the HmBRI D-E loop. The adjacent protomer is shown in orange and its residues are marked by a prime. Three structural water molecules are observed that stabilize the loop structure.

Mentions: Similarly to other archaeal proton pumps [10]–[13] and despite being heterologously expressed in a bacterium Escherichia coli, HmBRI assembles as a trimer in crystals (Figure 7A). The RMSD between the backbone heavy atoms positions in the HmBRI and HsBR trimers is ∼1.0 Å. This value reflexes the slightly different orientation of the HmBRI protomers in crystals, where the extracellular sides of the trimers align well, but the cytoplasmic sides are slightly displaced (Figure 7A). Such trimeric organization of HmBRI is similar to that of deltarhodopsin-3 [13], as the RMSD of atomic positions is ∼0.45 Å when either monomers or trimers are compared.


Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form.

Shevchenko V, Gushchin I, Polovinkin V, Round E, Borshchevskiy V, Utrobin P, Popov A, Balandin T, Büldt G, Gordeliy V - PLoS ONE (2014)

Structure of the HmBRI trimer and its D-E loop.(A) Comparison of the HmBRI trimer structure (green) with that of HsBR [23] (yellow). HmBRI trimer aligns well in the extracellular region, but the protomers are slightly rotated at the cytoplasmic side. (B) Magnification of the D-E loop. Unlike in other trimerizing retinylidene proteins, in HmBRI the loop is extended and makes contact to the adjacent protomer. (C) Wall-eyed stereogram of the HmBRI D-E loop. The adjacent protomer is shown in orange and its residues are marked by a prime. Three structural water molecules are observed that stabilize the loop structure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4257550&req=5

pone-0112873-g007: Structure of the HmBRI trimer and its D-E loop.(A) Comparison of the HmBRI trimer structure (green) with that of HsBR [23] (yellow). HmBRI trimer aligns well in the extracellular region, but the protomers are slightly rotated at the cytoplasmic side. (B) Magnification of the D-E loop. Unlike in other trimerizing retinylidene proteins, in HmBRI the loop is extended and makes contact to the adjacent protomer. (C) Wall-eyed stereogram of the HmBRI D-E loop. The adjacent protomer is shown in orange and its residues are marked by a prime. Three structural water molecules are observed that stabilize the loop structure.
Mentions: Similarly to other archaeal proton pumps [10]–[13] and despite being heterologously expressed in a bacterium Escherichia coli, HmBRI assembles as a trimer in crystals (Figure 7A). The RMSD between the backbone heavy atoms positions in the HmBRI and HsBR trimers is ∼1.0 Å. This value reflexes the slightly different orientation of the HmBRI protomers in crystals, where the extracellular sides of the trimers align well, but the cytoplasmic sides are slightly displaced (Figure 7A). Such trimeric organization of HmBRI is similar to that of deltarhodopsin-3 [13], as the RMSD of atomic positions is ∼0.45 Å when either monomers or trimers are compared.

Bottom Line: The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins.The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface.All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

View Article: PubMed Central - PubMed

Affiliation: Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany; Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia.

ABSTRACT
Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.

Show MeSH
Related in: MedlinePlus