1rkj
From Proteopedia
(New page: 200px<br /><applet load="1rkj" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rkj" /> '''Solution structure of the complex formed by ...) |
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'''Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target'''<br /> | '''Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Nucleolin is a 70 kDa multidomain protein involved in several steps of | + | Nucleolin is a 70 kDa multidomain protein involved in several steps of eukaryotic ribosome biogenesis. In vitro selection in combination with mutagenesis and structural analysis identified binding sites in pre-rRNA with the consensus (U/G)CCCG(A/G) in the context of a hairpin structure, the nucleolin recognition element (NRE). The central region of the protein contains four tandem RNA-binding domains (RBDs), of which the first two are responsible for the RNA-binding specificity and affinity for NREs. Here, we present the solution structure of the 28 kDa complex formed by the two N-terminal RNA-binding domains of nucleolin (RBD12) and a natural pre-rRNA target, b2NRE. The structure demonstrates that the sequence-specific recognition of the pre-rRNA NRE is achieved by intermolecular hydrogen bonds and stacking interactions involving mainly the beta-sheet surfaces of the two RBDs and the linker residues. A comparison with our previously determined NMR structure of RBD12 in complex with an in vitro selected RNA target, sNRE, shows that although the sequence-specific recognition of the loop consensus nucleotides is the same in the two complexes, they differ in several aspects. While the protein makes numerous specific contacts to the non-consensus nucleotides in the loop E motif (S-turn) in the upper part of the sNRE stem, nucleolin RBD12 contacts only consensus nucleotides in b2NRE. The absence of these upper stem contacts from the RBD12/b2NRE complex results in a much less stable complex, as demonstrated by kinetic analyses. The role of the loop E motif in high-affinity binding is supported by gel-shift analyses with a series of sNRE mutants. The less stable interaction of RBD12 with the natural RNA target is consistent with the proposed role of nucleolin as a chaperone that interacts transiently with pre-rRNA to prevent misfolding. |
==About this Structure== | ==About this Structure== | ||
| - | 1RKJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mesocricetus_auratus Mesocricetus auratus]. Full crystallographic information is available from [http:// | + | 1RKJ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mesocricetus_auratus Mesocricetus auratus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKJ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Feigon, J.]] | [[Category: Feigon, J.]] | ||
| - | [[Category: Finger, L | + | [[Category: Finger, L D.]] |
[[Category: Johansson, C.]] | [[Category: Johansson, C.]] | ||
[[Category: Kim, S.]] | [[Category: Kim, S.]] | ||
| - | [[Category: Laird-Offringa, I | + | [[Category: Laird-Offringa, I A.]] |
| - | [[Category: Mueller, T | + | [[Category: Mueller, T D.]] |
[[Category: Trantirek, L.]] | [[Category: Trantirek, L.]] | ||
[[Category: protein-rna complex]] | [[Category: protein-rna complex]] | ||
[[Category: rbd]] | [[Category: rbd]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:51:52 2008'' |
Revision as of 12:51, 21 February 2008
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Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target
Overview
Nucleolin is a 70 kDa multidomain protein involved in several steps of eukaryotic ribosome biogenesis. In vitro selection in combination with mutagenesis and structural analysis identified binding sites in pre-rRNA with the consensus (U/G)CCCG(A/G) in the context of a hairpin structure, the nucleolin recognition element (NRE). The central region of the protein contains four tandem RNA-binding domains (RBDs), of which the first two are responsible for the RNA-binding specificity and affinity for NREs. Here, we present the solution structure of the 28 kDa complex formed by the two N-terminal RNA-binding domains of nucleolin (RBD12) and a natural pre-rRNA target, b2NRE. The structure demonstrates that the sequence-specific recognition of the pre-rRNA NRE is achieved by intermolecular hydrogen bonds and stacking interactions involving mainly the beta-sheet surfaces of the two RBDs and the linker residues. A comparison with our previously determined NMR structure of RBD12 in complex with an in vitro selected RNA target, sNRE, shows that although the sequence-specific recognition of the loop consensus nucleotides is the same in the two complexes, they differ in several aspects. While the protein makes numerous specific contacts to the non-consensus nucleotides in the loop E motif (S-turn) in the upper part of the sNRE stem, nucleolin RBD12 contacts only consensus nucleotides in b2NRE. The absence of these upper stem contacts from the RBD12/b2NRE complex results in a much less stable complex, as demonstrated by kinetic analyses. The role of the loop E motif in high-affinity binding is supported by gel-shift analyses with a series of sNRE mutants. The less stable interaction of RBD12 with the natural RNA target is consistent with the proposed role of nucleolin as a chaperone that interacts transiently with pre-rRNA to prevent misfolding.
About this Structure
1RKJ is a Single protein structure of sequence from Mesocricetus auratus. Full crystallographic information is available from OCA.
Reference
Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target., Johansson C, Finger LD, Trantirek L, Mueller TD, Kim S, Laird-Offringa IA, Feigon J, J Mol Biol. 2004 Apr 2;337(4):799-816. PMID:15033352
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