NORMAL GENOMIC

• Mantovani A, Garlanda C, Doni A, Bottazzi B
• Pentraxins in innate immunity: from C-reactive protein to the longpentraxin PTX3.
• J Clin Immunol. 2008; 28: 1-13
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• Pentraxins are a family of multimeric pattern-recognition proteins highlyconserved in evolution. Based on the primary structure of the subunit, thepentraxins are divided into two groups: short pentraxins and longpentraxins. C-reactive protein and serum amyloid P-component are classicshort pentraxins produced in the liver, whereas the prototype of the longpentraxin family is PTX3. Innate immunity cells and vascular cells producePTX3 in response to proinflammatory signals and Toll-like receptorengagement. PTX3 interacts with several ligands, including growth factors,extracellular matrix components, and selected pathogens, playing a role incomplement activation, facilitating pathogen recognition, and acting as apredecessor of antibodies. In addition, PTX3 is essential in femalefertility acting on the assembly of the cumulus oophorus extracellularmatrix. Thus, PTX3 is a multifunctional soluble pattern recognitionreceptor acting as a nonredundant component of the humoral arm of innateimmunity and involved in tuning inflammation, in matrix deposition andfemale fertility. Evidence suggests that PTX3 is a useful new serologicalmarker, rapidly reflecting tissue inflammation and damage under diverseclinical conditions.

• Carlson CB, Lawler J, Mosher DF
• Structures of thrombospondins.
• Cell Mol Life Sci. 2008; 65: 672-86
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• Thrombospondins are large secreted, multimodular, calcium-bindingglycoproteins that have complex roles in mediating cellular processes.Determination of high-resolution structures of thrombospondins hasrevealed unique and interesting protein motifs. Here, we review thisprogress and discuss implications for function. By combining structures ofmodules from thrombospondins and related extracellular proteins it is nowpossible to prepare an overall model of the structure of thrombospondin-1and thrombospondin-2 and discern features of other thrombospondins. (Partof a multi-author Review).

• Seigneuret M
• Complete predicted three-dimensional structure of the facilitatortransmembrane protein and hepatitis C virus receptor CD81: conserved andvariable structural domains in the tetraspanin superfamily.
• Biophys J. 2006; 90: 212-27
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• Tetraspanins are a superfamily of transmembrane proteins implicated incellular development, motility, and activation through their interactionswith a large range of proteins and with specific membrane microdomains.The complete three-dimensional structure of the tetraspanin CD81 has beenpredicted by molecular modeling and from the crystallographic structure ofthe EC2 large extracellular domain. Periodicity of sequence conservation,homology modeling, secondary structure prediction, and protein dockingwere used. The transmembrane domain appears organized as a four-strandedleft-handed coiled coil directly connecting to two helices of the EC2. Asmaller extracellular loop EC1 contains a small largely hydrophobicbeta-strand that packs in a conserved hydrophobic groove of the EC2. Thepalmitoylable intracellular N-terminal segment forms an amphipathicmembrane-parallel helix. Structural variability occurs mainly in anhypervariable subdomain of the EC2 and in intracellular regions.Therefore, the variable interaction selectivity of tetraspanins originatesboth from sequence variability within structurally conserved domains andfrom the occurrence of small structurally variable domains. In CD81 andother tetraspanins, the numerous membrane-exposed aromatic residues areasymmetrically clustered and protrude on one side of the transmembranedomain. This may represent a functional specialization of these two sidesfor interactions with cholesterol, proteins, or membrane microdomains.

• Wang G, Wylie GP, Twigg PD, Caspar DL, Murphy JR, Logan TM
• Solution structure and peptide binding studies of the C-terminal srchomology 3-like domain of the diphtheria toxin repressor protein.
• Proc Natl Acad Sci U S A. 1999; 96: 6119-24
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• The diphtheria toxin repressor (DtxR) is the best-characterized member ofa family of homologous proteins that regulate iron uptake and virulencegene expression in the Gram-positive bacteria. DtxR contains two domainsthat are separated by a short, unstructured linker. The N-terminal domainis structurally well-defined and is responsible for Fe2+ binding,dimerization, and DNA binding. The C-terminal domain adopts a fold similarto eukaryotic Src homology 3 domains, but the functional role of theC-terminal domain in repressor activity is unknown. The solution structureof the C-terminal domain, consisting of residues N130-L226 plus a13-residue N-terminal extension, has been determined by using NMRspectroscopy. Residues before A147 are highly mobile and adopt a randomcoil conformation, but residues A147-L226 form a single structured domainconsisting of five beta-strands and three helices arranged into apartially orthogonal, two-sheet beta-barrel, similar to the structureobserved in the crystalline Co2+ complex of full-length DtxR. Chemicalshift perturbation studies demonstrate that a proline-rich peptidecorresponding to residues R125-G139 of intact DtxR binds to the C-terminaldomain in a pocket formed by residues in beta-strands 2, 3, and 5, andhelix 3. Binding of the proline-rich peptide by the C-terminal domain ofDtxR presents an example of peptide binding by a prokaryotic Src homology3-like protein. The results of this study, combined with previous x-raystudies of intact DtxR, provide insights into a possible biologicalfunction of the C-terminal domain in regulating repressor activity.

• Rubio N, Sharp PM, Rits M, Zahedi K, Whitehead AS
• Structure, expression, and evolution of guinea pig serum amyloid Pcomponent and C-reactive protein.
• J Biochem. 1993; 113: 277-84
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• The structure and expression of the pentraxins, serum amyloid P component(SAP), and C-reactive protein (CRP), have been investigated in the guineapig. Northern blot analysis of hepatic RNA from animals in which acuteinflammation had been induced by intraperitoneal injection ofthioglycollate established that neither SAP or CRP is a major acute phasereactant in the guinea pig. Genomic clones of SAP and CRP were isolatedand sequenced, and the gene and the derived protein sequences werecompared with other mammalian homologues. Both genes have organizationstypical of the pentraxin genes of other species, but some differences weredefined in the regions that potentially determine the capacity of thepentraxin gene to be induced during acute inflammation. Nucleotidesubstitutions in coding regions have occurred at similar rates in the twopentraxin genes. Nonsynonymous substitution rates indicate that SAP andCRP are subject to similar, relatively low levels of constraint; at theamino acid sequence level the rate of evolution is approximately tworeplacements per site per 10(9) years. An estimate of the phylogeneticrelationship among the pentraxin genes suggests that SAP and CRP arose asthe result of a gene duplication event that occurred very early inmammalian evolution, but subsequent to the divergence of the reptilianancestors of the mammalian and avian lineages. This raises doubts aboutthe identity of proteins from fish, which have been previouslycharacterized as CRP and SAP.