About: Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases

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About: Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases
Creator	Lang, Dorothy Zemla, A Zhou, C
Source	PMC
abstract	RNA-dependent RNA polymerase (RdRp) is essential to viral replication and is therefore one of the primary targets of countermeasures against these dangerous infectious agents. Development of broad-spectrum therapeutics targeting polymerases has been hampered by the extreme sequence variability of these sequences. RdRps range in length from 400–800 residues, yet contain only ∼20 residues that are conserved in most species. In this study, we made structure-based comparisons that are independent of sequence composition using a recently developed algorithm. We identified residue-to-residue correspondences of multiple protein structures and created (two-dimensional) structure-based alignment maps of 37 polymerase structures that provide both sequence and structure details. Using these maps, we determined that ∼75% of each polymerase species consists of seven protein segments, each of which has high structural similarity to segments in other species, though they are widely divergent in sequence composition and order. We define each of these segments as a ‘homomorph’, and each includes (though most are much larger than) the well-known conserved polymerase motifs. All homomorphs contact the template tunnel or nucleoside triphosphate (NTP) entry tunnel and the exterior of the protein, suggesting they constitute a structural and functional skeleton common among the polymerases.
has issue date	2012-12-25(xsd:dateTime)
bibo:doi	10.1093/nar/gks1251
bibo:pmid	23275546
has license	cc-by-nc
sha1sum (hex)	8dc8c40ee8b61c5660b15c9e81e928eb3dc44ee5
schema:url	https://doi.org/10.1093/nar/gks1251
resource representing a document's title	Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases
has PubMed Central identifier	PMC3561941
has PubMed identifier	23275546
schema:publication	Nucleic Acids Res
resource representing a document's body	covid:8dc8c40ee8b61c5660b15c9e81e928eb3dc44ee5#body_text
is schema:about of	named entity 'RNA' named entity 'EXTERIOR' named entity 'MUCH' named entity 'ORDER' named entity 'INDEPENDENT OF' named entity 'PROTEIN STRUCTURES' named entity 'RANGE' named entity 'MOTIFS' named entity 'ALIGNMENT' named entity 'CONTAIN' named entity 'MULTIPLE' named entity 'VARIABILITY' named entity 'USING' named entity 'ESSENTIAL' named entity 'DETAILS' named entity 'POLYMERASE' named entity 'ONE OF' named entity 'SEQUENCE COMPOSITION' named entity 'THESE' named entity 'PROVIDE' named entity 'LARGER' named entity 'KNOWN' named entity 'STRUCTURAL' named entity 'PROTEIN ' named entity 'INCLUDES' named entity 'RESIDUE' named entity 'COMMON' named entity 'DETERMINED' named entity 'SEVEN' named entity 'protein' named entity 'ENTRY' named entity 'LINK' named entity 'IDENTIFIED' named entity 'TUNNEL' named entity 'VIRAL REPLICATION' named entity 'DEPENDENT' named entity 'RNA-DEPENDENT RNA POLYMERASE' named entity 'SIMILARITY' named entity 'EXTREME' named entity 'STUDY' named entity 'HIGH' named entity 'SIMILAR' named entity 'POLYMERASES' named entity 'HIGHLY' named entity 'TEMPLATE' named entity 'NTP' named entity 'STRUCTURAL' named entity 'TUNNEL' named entity 'EXTERIOR' named entity 'STRUCTURE' named entity 'CONTACT' named entity 'RECENTLY' named entity '800' named entity 'BROAD' named entity 'THERAPEUTICS' named entity 'PROTEIN' named entity 'SEGMENTS' named entity 'ALGORITHM' named entity '400' named entity 'FUNCTIONAL' named entity 'MAPS' named entity 'BASED' named entity 'SURFACE' named entity 'STRUCTURES' named entity 'NUCLEOSIDE TRIPHOSPHATE' named entity 'CREATED' named entity 'CONSERVED' named entity 'SEQUENCE' named entity 'SPECTRUM' named entity 'TARGETING' named entity 'PRIMARY' named entity 'FRAMES' named entity 'TARGETS' named entity 'ENTRY' named entity 'POLYMERASES' named entity 'OF EACH' named entity 'SPECIES' named entity 'INFECTIOUS AGENTS' named entity 'DEVELOPMENT'

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