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X-ray crystallographic refinement and analysis of the Haloarcula marismortui large ribosomal subunit

Record Type:	Electronic resources : Monograph/item
Title/Author:	X-ray crystallographic refinement and analysis of the Haloarcula marismortui large ribosomal subunit
Author:	Klein, Daniel Joseph.
Description:	184 p.
Notes:	Adviser: Thomas Steitz.
Notes:	Source: Dissertation Abstracts International, Volume: 65-03, Section: B, page: 1307.
Contained By:	Dissertation Abstracts International65-03B.
Subject:	Chemistry, Biochemistry.
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3125231
ISBN:	0496725211

X-ray crystallographic refinement and analysis of the Haloarcula marismortui large ribosomal subunit
Klein, Daniel Joseph.

X-ray crystallographic refinement and analysis of the Haloarcula marismortui large ribosomal subunit [electronic resource] - 184 p.

Adviser: Thomas Steitz.

Thesis (Ph.D.)--Yale University, 2004.

Our analysis addresses three features of the large ribosomal subunit that account for its structural stability: (i) the formation of small RNA secondary structural motifs, (ii) interactions between RNA and ribosomal proteins, and (iii) interactions between RNA and metal ions. A new RNA structural motif, the K-turn, has been identified. The K-turn's structure is characterized by a kinked phosphodiester backbone, an asymmetric internal loop adjacent to conserved sheared G-A base pairs, and an A-minor interaction between its two helical stems. A consensus secondary structure derived from six K-turns in 23S rRNA predicts the motif's presence in RNAs of unknown structure. Despite having similar structures, five K-turns in 23S rRNA interact with nine proteins in very different ways. In general, the interactions between rRNA and the 29 ribosomal proteins are idiosyncratic. Electrostatic interactions are observed between RNA phosphate groups and protein arginine and lysine residues, especially those in conserved protein tails. Base recognition occurs via both the minor groove and widened major groove of RNA helices, through hydrophobic binding pockets on proteins that capture bulged nucleotides, and through insertion of amino acids into hydrophobic crevices in the RNA. Primary binding sites are identified on contiguous RNA for 20 proteins of the large ribosomal subunit, which suggest the order of assembly for some proteins and that the protein tails fold cooperatively with RNA. Finally, this study is the first to identify binding sites for metal ions in the ribosome. Metal ions stabilize the tertiary and quaternary structure of the ribosome and are abundant in the peptidyl transferase center of 23S rRNA, which suggests that a primordial all-RNA ribosome could not have folded without metal ions.

ISBN: 0496725211Subjects--Topical Terms:

226900
Chemistry, Biochemistry.

X-ray crystallographic refinement and analysis of the Haloarcula marismortui large ribosomal subunit
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502 $a Thesis (Ph.D.)--Yale University, 2004.
520 # $a Our analysis addresses three features of the large ribosomal subunit that account for its structural stability: (i) the formation of small RNA secondary structural motifs, (ii) interactions between RNA and ribosomal proteins, and (iii) interactions between RNA and metal ions. A new RNA structural motif, the K-turn, has been identified. The K-turn's structure is characterized by a kinked phosphodiester backbone, an asymmetric internal loop adjacent to conserved sheared G-A base pairs, and an A-minor interaction between its two helical stems. A consensus secondary structure derived from six K-turns in 23S rRNA predicts the motif's presence in RNAs of unknown structure. Despite having similar structures, five K-turns in 23S rRNA interact with nine proteins in very different ways. In general, the interactions between rRNA and the 29 ribosomal proteins are idiosyncratic. Electrostatic interactions are observed between RNA phosphate groups and protein arginine and lysine residues, especially those in conserved protein tails. Base recognition occurs via both the minor groove and widened major groove of RNA helices, through hydrophobic binding pockets on proteins that capture bulged nucleotides, and through insertion of amino acids into hydrophobic crevices in the RNA. Primary binding sites are identified on contiguous RNA for 20 proteins of the large ribosomal subunit, which suggest the order of assembly for some proteins and that the protein tails fold cooperatively with RNA. Finally, this study is the first to identify binding sites for metal ions in the ribosome. Metal ions stabilize the tertiary and quaternary structure of the ribosome and are abundant in the peptidyl transferase center of 23S rRNA, which suggests that a primordial all-RNA ribosome could not have folded without metal ions.
520 # $a The crystal structure of the Haloarcula marismortui large ribosomal subunit has been refined to a free R-factor of 22.2% at 2.4 A resolution. During refinement, the structure of the Helix 43--44 region of 23S rRNA was determined, modified nucleotides in 23S rRNA were identified, the structures of segments of proteins L10, L11, and L39e were determined, and a conserved disordered loop was identified in protein L10e that is located close to the peptidyl transferase site.
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