A specific amino acid binding site composed of RNA

Science ◽  
1988 ◽  
Vol 240 (4860) ◽  
pp. 1751-1758 ◽  
Author(s):  
M Yarus
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Specific Amino Acid ◽  
Reversible Binding ◽  
Amino Acid Interaction ◽  
Precursor Rna ◽  
Amino Acid Binding ◽  
Natural Amino Acids ◽  
Ribosomal Precursor ◽  
Self Splicing

A specific, reversible binding site for a free amino acid is detectable on the intron of the Tetrahymena self-splicing ribosomal precursor RNA. The site selects arginine among the natural amino acids, and prefers the L- to the D-amino acid. The dissociation constant is in the millimolar range, and amino acid binding is at or in the catalytic rG splicing substrate site. Occupation of the G site by L-arginine therefore inhibits splicing by inhibiting the binding of rG, without inhibition of later reactions in the splicing reaction sequence. Arginine binding specificity seems to be directed at the side chain and the guanidino radical, and the alpha-amino and carboxyl groups are dispensable for binding. The arginine site can be placed within the G site by structural homology, with consequent implications for RNA-amino acid interaction, for the origin of the genetic code, for control of RNA activities, and for further catalytic capabilities for RNA.

Group II introns deleted for multiple substructures retain self-splicing activity

1992 ◽  
Vol 12 (5) ◽  
pp. 1950-1958
Author(s):  
J L Koch ◽  
S C Boulanger ◽  
S D Dib-Hajj ◽  
S K Hebbar ◽  
P S Perlman
Keyword(s):  
Binding Site ◽  
Splice Junction ◽  
Group Ii Introns ◽  
Splice Site Selection ◽  
Catalytic Core ◽  
Single Deletion ◽  
Group Ii ◽  
Precursor Rna ◽  
Self Splicing

Group II introns can be folded into highly conserved secondary structures with six major substructures or domains. Domains 1 and 5 are known to play key roles in self-splicing, while the roles of domains 2, 3, 4, and 6 are less clear. A trans assay for domain 5 function has been developed which indicates that domain 5 has a binding site on the precursor RNA that is not predicted from any secondary structure element. In this study, the self-splicing group II intron 5 gamma of the coxI gene of yeast mitochondrial DNA was deleted for various intron domains, singly and in combinations. Those mutant introns were characterized for self-splicing reactions in vitro as a means of locating the domain 5 binding site. A single deletion of domain 2, 3, 4, or 6 does not block in vitro reactions at either splice junction, though the deletion of domain 6 reduces the fidelity of 3' splice site selection somewhat. Even the triple deletion lacking domains 2, 4, and 6 retains some self-splicing activity. The deletion of domains 2, 3, 4, and 6 blocks the reaction at the 3' splice junction but not at the 5' junction. From these results, we conclude that the binding site for domain 5 is within domain 1 and that the complex of 5' exon, domain 1, and domain 5 (plus short connecting sequences) constitutes the essential catalytic core of this intron.

scholarly journals Binding of high-molecular-mass kininogen to the Apple 1 domain of factor XI is mediated in part by Val64 and Ile77

1994 ◽  
Vol 304 (3) ◽  
pp. 715-721 ◽  
Author(s):  
F S Seaman ◽  
F A Baglia ◽  
J A Gurr ◽  
B A Jameson ◽  
P N Walsh
Keyword(s):  
Amino Acid ◽  
Molecular Mass ◽  
Binding Site ◽  
Expression System ◽  
High Molecular Mass ◽  
Amino Acid Residues ◽  
Factor Xi ◽  
Specific Amino Acid ◽  
Conformationally Constrained ◽  
A1 Domain

We have previously demonstrated the presence of a binding site for high-molecular-mass kininogen (HK), spanning residues Val59-Lys83, in the first Apple (A1) domain in the heavy-chain region of factor XI. We have now prepared conformationally constrained synthetic peptides and recombinant A1 domain (rA1) constructs to identify the specific amino acid residues that constitute the HK-binding site. Expression of the A1 domain (Glu1-Ser90) was achieved in a bacterial expression system following PCR amplification of the A1 domain from factor XI cDNA and ligation into an expression plasmid. The rA1 inhibited factor XI binding to HK [Ki approximately (2-3) x 10(-7) M] in a manner indistinguishable from purified factor XI, indicating that all the information necessary for binding HK is contained within the A1 domain. To identify specific amino acid residues involved in binding HK, conformationally constrained peptides were synthesized containing conservative amino acid substitutions at residues suspected to contain side chains involved in binding, including Val64-->Ala, Glu66-->Ala, Arg73-->Ala and Ile77-->Ala. Because normal results were obtained with all peptides with the exception of Val64-->Ala and Ile77-->Ala, which failed to compete normally with factor XI for binding to HK, we prepared two mutant rA1 domains (Val64-->Ala and Ile77-->Ala) by PCR-based site-directed mutagenesis, both of which exhibited diminished capacity to inhibit factor XI binding to HK. Competition studies with prekallikrein (PK) and a PK-dependent synthetic peptide suggested that PK and factor XI have a common surface in the A1 domain for binding HK of which Val64 is a part. We conclude that the binding of factor XI to HK is mediated at least in part by Val64 and Ile77 in the A1 domain of factor XI.

scholarly journals The Venus Fly Trap Domain of the Extracellular Ca2+-sensing Receptor Is Required for l-Amino Acid Sensing

2004 ◽  
Vol 279 (50) ◽  
pp. 51739-51744 ◽  
Author(s):  
Hee-Chang Mun ◽  
Alison H. Franks ◽  
Emma L. Culverston ◽  
Karen Krapcho ◽  
Edward F. Nemeth ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Binding Site ◽  
Hek293 Cells ◽  
Transmembrane Region ◽  
Rich Region ◽  
Metabotropic Glutamate ◽  
C Terminus ◽  
Amino Acid Binding ◽  
Amino Acid Sensing

We previously demonstrated that the human calcium-sensing receptor (CaR) is allosterically activated byl-amino acids (Conigrave, A. D., Quinn, S. J., and Brown, E. M. (2000)Proc. Natl. Acad. Sci. U. S. A.97, 4814–4819). However, the domain-based location of amino acid binding has been uncertain. We now show that the Venus Fly Trap (VFT) domain of CaR, but none of its other major domains, is required for amino acid sensing. Several constructs were informative when expressed in HEK293 cells. First, the wild-type CaR exhibited allosteric activation byl-amino acids as previously observed. Second, two CaR-mGlu chimeric receptor constructs that retained the VFT domain of CaR, one containing the extracellular Cys-rich region of CaR and the other containing the Cys-rich region of the rat metabotropic glutamate type-1 (mGlu-1) receptor, together with the rat mGlu-1 transmembrane region and C-terminal tail, retained amino acid sensing. Third, a CaR lacking residues 1–599 of the N-terminal extracellular head but retaining an intact CaR transmembrane region and a functional but truncated C terminus (headless-T903 CaR) failed to respond tol-amino acids but retained responsiveness to the type-II calcimimetic NPS R-467. Finally, a T903 CaR control that retained an intact N terminus also retainedl-amino acid sensing. Taken together, the data indicate that the VFT domain of CaR is necessary forl-amino acid sensing and are consistent with the hypothesis that the VFT domain is the site ofl-amino acid binding. The findings support the concept that the mGlu-1 amino acid binding site forl-glutamate is conserved as anl-amino acid binding site in its homolog, the CaR.

Transport and signaling via the amino acid binding site of the yeast Gap1 amino acid transceptor

2008 ◽  
Vol 5 (1) ◽  
pp. 45-52 ◽  
Author(s):  
Griet Van Zeebroeck ◽  
Beatriz Monge Bonini ◽  
Matthias Versele ◽  
Johan M Thevelein
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Amino Acid Binding ◽  
Amino Acid Transceptor

scholarly journals Localization of striatal excitatory amino acid binding site subtypes to striatonigral projection neurons

1992 ◽  
Vol 594 (1) ◽  
pp. 165-170 ◽  
Author(s):  
Sara J. Tallaksen-Greene ◽  
Ronald G. Wiley ◽  
Roger L. Albin
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Excitatory Amino Acid ◽  
Projection Neurons ◽  
Amino Acid Binding

scholarly journals Sulfadoxine Resistance in Plasmodium vivax Is Associated with a Specific Amino Acid in Dihydropteroate Synthase at the Putative Sulfadoxine-Binding Site

2004 ◽  
Vol 48 (6) ◽  
pp. 2214-2222 ◽  
Author(s):  
Michael Korsinczky ◽  
Katja Fischer ◽  
Nanhua Chen ◽  
Joanne Baker ◽  
Karl Rieckmann ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Plasmodium Vivax ◽  
Binding Sites ◽  
Protein Sequence ◽  
Three Dimensional ◽  
Specific Amino Acid ◽  
Dihydropteroate Synthase ◽  
Contact Residues ◽  
Amino Acid Mutations

ABSTRACT Sulfadoxine is predominantly used in combination with pyrimethamine, commonly known as Fansidar, for the treatment of Plasmodium falciparum. This combination is usually less effective against Plasmodium vivax, probably due to the innate refractoriness of parasites to the sulfadoxine component. To investigate this mechanism of resistance by P. vivax to sulfadoxine, we cloned and sequenced the P. vivax dhps (pvdhps) gene. The protein sequence was determined, and three-dimensional homology models of dihydropteroate synthase (DHPS) from P. vivax as well as P. falciparum were created. The docking of sulfadoxine to the two DHPS models allowed us to compare contact residues in the putative sulfadoxine-binding site in both species. The predicted sulfadoxine-binding sites between the species differ by one residue, V585 in P. vivax, equivalent to A613 in P. falciparum. V585 in P. vivax is predicted by energy minimization to cause a reduction in binding of sulfadoxine to DHPS in P. vivax compared to P. falciparum. Sequencing dhps genes from a limited set of geographically different P. vivax isolates revealed that V585 was present in all of the samples, suggesting that V585 may be responsible for innate resistance of P. vivax to sulfadoxine. Additionally, amino acid mutations were observed in some P. vivax isolates in positions known to cause resistance in P. falciparum, suggesting that, as in P. falciparum, these mutations are responsible for acquired increases in resistance of P. vivax to sulfadoxine.

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