SCOP: a Structural Classification of Proteins database

Hubbard, Tim; Ailey, Bart; Brenner, Steven E.; Murzin, Alexey G.; Chothia, Cyrus

doi:10.1093/nar/25.1.236

Cited by 499 publications

(213 citation statements)

References 10 publications

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“…Upon interruption of this sheet extension by a ␤-bulge the polypeptide chain crosses over to become part of the AG-FCCЈ sheet (residues 91-96). Such a sheet crossover does not occur in other Ig domains of the I-set as classified by the SCOP (structural classification of proteins) data base (40) and to the best of our knowledge has not been observed in any other Ig superfamily domain fold so far. The second Ig domain spans residues 97-182, and strand A starts at residue 100.…”

Section: Resultsmentioning

confidence: 61%

Ligand Recognition and Homophilic Interactions in Tyro3

Heiring

Dahlbäck

Muller

2004

Journal of Biological Chemistry

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The receptor Tyro3 together with Axl and Mer form the Axl/Tyro3 family of receptor tyrosine kinases. Members of this family play essential roles in spermatogenesis, immunoregulation, and phagocytosis. Gas6, the product of growth arrest-specific gene, activates the kinase activity of all three receptors. Here, we report the first biochemical and structural characterization of a member of this family, namely of a fragment spanning the two N-terminal Ig domains of the extracellular part of human Tyro3. Its ligand binding specificity profile is identical to the activation profile of the native receptor. The 1.95-Å crystal structure suggests a common ligandbinding site in this receptor family located at the interface of the Ig domains and unusually rich in cis-prolines. Furthermore, both in the crystal and in solution we observed the ligand-independent dimerization of the receptor fragment. This homophilic interaction emphasizes previous functional reports, which hinted that in addition to signal transduction, members of this family of receptors might participate in cell adhesion.

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Section: Resultsmentioning

confidence: 61%

Ligand Recognition and Homophilic Interactions in Tyro3

Heiring

Dahlbäck

Muller

2004

Journal of Biological Chemistry

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“…The three-dimensional structure for the VNG1688C ortholog MTH1 in Methanothermobacter thermoautotrophicus (PDB: 1k3r) matches two superfamilies in SCOP (Hubbard et al 1997), b.40.4 (a nucleic acid binding domain) and c.116.1 (a SAMdependent methytransferases). Like VNG1688C, MTH1 is also encoded immediately upstream to the ribosomal protein operon (Smith et al 1997;Ng et al 2000).…”

Section: Ribosome Biogenesis And/or Function In Halobacterium Nrc-1 Mmentioning

confidence: 94%

Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic ArchaeonHalobacterium NRC-1

Baliga¹,

Bjork²,

Bonneau³

et al. 2004

Genome Res.

137

142

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We report a remarkably high UV-radiation resistance in the extremely halophilic archaeon Halobacterium NRC-1 withstanding up to 110 J/m 2 with no loss of viability. Gene knockout analysis in two putative photolyase-like genes (phr1 and phr2) implicated only phr2 in photoreactivation. The UV-response was further characterized by analyzing simultaneously, along with gene function and protein interactions inferred through comparative genomics approaches, mRNA changes for all 2400 genes during light and dark repair. In addition to photoreactivation, three other putative repair mechanisms were identified including d(CTAG) methylation-directed mismatch repair, four oxidative damage repair enzymes, and two proteases for eliminating damaged proteins. Moreover, a UV-induced down-regulation of many important metabolic functions was observed during light repair and seems to be a phenomenon shared by all three domains of life. The systems analysis has facilitated the assignment of putative functions to 26 of 33 key proteins in the UV response through sequence-based methods and/or similarities of their predicted three-dimensional structures to known structures in the PDB. Finally, the systems analysis has raised, through the integration of experimentally determined and computationally inferred data, many experimentally testable hypotheses that describe the metabolic and regulatory networks of Halobacterium NRC-1.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GEO under accession no. GSE1040.]Biological systems have evolved mechanisms to appropriately respond to environmental stresses that can damage proteins and DNA. Halobacterium NRC-1, for example, has evolved the capacity to withstand up to 4.5M salinity, ultraviolet radiation (UV), and oxidative stress in its natural environment. One such adaptation, the high-density of acidic residues on the surface of almost all halobacterial proteins, is believed to stabilize protein structure and function in high salt (Kennedy et al. 2001). It can also physically relocate to favorable environments using sensors for light, oxygen, and nutrients, and produce energy through respiration, fermentation, or phototrophy (Ng et al. 2000). We have previously reported a response mechanism in Halobacterium NRC-1 that coordinately regulates phototrophy and arginine fermentation, two major sources for anaerobic energy production. The effects of perturbing the function of a regulator in this response mechanism were observed throughout the metabolic network (Baliga et al. 2002).Systems approaches allow us to raise a whole series of hypotheses regarding the behavior of a system in response to a defined experimental perturbation. These hypotheses then stimulate iterative cycles of perturbations and analyses to verify these hypotheses. Here, we report a systems-level study on the behavior of Halobacterium NRC-1 upon UV-C irradiation. Shortwave ultraviolet light (UV-C) induces two types of mutagenic lesions in DNA-cyclobutane pyrimid...

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“…Whereas all three families have similar β-barrel topologies, the details of the strand geometry of the barrels suggest that the three different families probably did not diverge from a common ancestor. SCOP [11] places the viral proteases in the same homologous superfamily as trypsin, perhaps due to their similar functions. Thus, the inference of homology -that two proteins share a common ancestor rather than arising independently -is based on both the degree of similarity that they share and some sense of how unlikely it is that this similarity could have arisen independently.…”

Section: Homology and Statistical Significance -The Argument From Parmentioning

confidence: 99%

The limits of protein sequence comparison?

Pearson

Sierk

2005

Current Opinion in Structural Biology

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Modern sequence alignment algorithms are used routinely to identify homologous proteins, proteins that share a common ancestor. Homologous proteins always share similar structures and often have similar functions. Over the past 20 years, sequence comparison has become both more sensitive, largely because of profile-based methods, and more reliable, because of more accurate statistical estimates. As sequence and structure databases become larger, and comparison methods become more powerful, reliable statistical estimates will become even more important for distinguishing similarities that are due to homology from those that are due to analogy (convergence). The newest sequence alignment methods are more sensitive than older methods, but more accurate statistical estimates are needed for their full power to be realized.

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SCOP: a Structural Classification of Proteins database

Cited by 499 publications

References 10 publications

Ligand Recognition and Homophilic Interactions in Tyro3

Ligand Recognition and Homophilic Interactions in Tyro3

Systems Level Insights Into the Stress Response to UV Radiation in the Halophilic ArchaeonHalobacterium NRC-1

The limits of protein sequence comparison?

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