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Model Structure of the Ompα Rod, a Parallel Four-stranded Coiled Coil from the Hyperthermophilic EubacteriumThermotoga maritima
- Source :
- Journal of Molecular Biology. 248:180-189
- Publication Year :
- 1995
- Publisher :
- Elsevier BV, 1995.
-
Abstract
- Omp alpha is an outer-membrane protein that spans the periplasmic space of the hyperthermophilic eubacterium Thermotoga maritima. The molecule contains a globular head with an apparent diameter of 8 nm and a rod-shaped tail of 40 nm length. The sequence of the globular domain is homologous to a conserved region of cell wall-bound proteins and probably attaches Omp alpha to the peptidoglycan. The sequence of the rod domain resembles that of coiled coil proteins and ends in a transmembrane segment that anchors Omp alpha to the outer membrane. We have analysed Omp alpha by scanning transmission electron microscopy (STEM) and by statistical sequence analysis methods. The Omp alpha rod is a tetramer with an unusual periodicity of hydrophobic residues close to 3.6 that differs from the 3.5 periodicity of canonical coiled coils. This is due to periodic omissions of three residues in the heptad repeat pattern ("stutters") whose effect is to locally distort the packing of hydrophobic layers in the core of the coiled coil. Residues in position alpha are shifted to occupy a position halfway between positions alpha and d (x layers) and residues in positions d and e are shifted so that both participate in core packing interactions (da layers). Such distorted layers are frequently found in helical bundles and are characteristic of helices that do not undergo supercoiling. The only homo-oligomeric coiled coil of known structure which contains x and da layers is the three-stranded coiled coil of influenza haemagglutinin. Using geometric constraints derived from this structure, we have built a model for the Omp alpha rod in which the helices have a crossing angle of less than 15 degrees and maintain a residual degree of supercoiling with a pitch of approximately 40 nm. Our analysis of distorted layers in the hydrophobic core of coiled coils and helical bundles shows that stutters must not be viewed as discontinuities but rather as a departure from the canonical "knobs-into-holes" packing that allows helices to interact at a low angle without supercoiling. Although stutters have been considered to weaken helical interactions, their occurrence in a rigid, highly thermostable coiled coil indicates that this may not be generally true. Our analysis also indicates that skips and stutters are two different conventions for describing the same underlying structural feature.
- Subjects :
- Microscopy, Electron, Scanning Transmission
Models, Molecular
Hot Temperature
Molecular Sequence Data
Protein Sorting Signals
Biology
Crystallography, X-Ray
Protein Structure, Secondary
Protein structure
Structural Biology
Animals
Amino Acid Sequence
Molecular Biology
Peptide sequence
Coiled coil
Gram-Negative Anaerobic Bacteria
Sequence Homology, Amino Acid
Periplasmic space
biology.organism_classification
Transmembrane domain
Crystallography
Heptad repeat
Thermotoga maritima
DNA supercoil
Software
Bacterial Outer Membrane Proteins
Subjects
Details
- ISSN :
- 00222836
- Volume :
- 248
- Database :
- OpenAIRE
- Journal :
- Journal of Molecular Biology
- Accession number :
- edsair.doi.dedup.....55c80b7858aa7348e6cb51a6b2dbb7df