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PDBsum entry 1m5o

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protein dna_rna metals Protein-protein interface(s) links
Translation/RNA PDB id
1m5o
Jmol
Contents
Protein chain
92 a.a. *
DNA/RNA
Metals
_CA ×37
Waters ×198
* Residue conservation analysis
PDB id:
1m5o
Name: Translation/RNA
Title: Transition state stabilization by a catalytic RNA
Structure: RNA substrate. Chain: a, d. Engineered: yes. RNA hairpin ribozyme. Chain: b, e. Engineered: yes. U1 small nuclear ribonucleoprotein a. Chain: c, f. Fragment: u1a RNA binding domain.
Source: Synthetic: yes. Other_details: this sequence occurs naturally in satellite tobacco ringspot virus. Homo sapiens. Human. Organism_taxid: 9606. Gene: snrpa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.20Å     R-factor:   0.229     R-free:   0.264
Authors: P.B.Rupert,A.P.Massey,S.T.Sigurdsson,A.R.Ferre-D'Amare
Key ref:
P.B.Rupert et al. (2002). Transition state stabilization by a catalytic RNA. Science, 298, 1421-1424. PubMed id: 12376595 DOI: 10.1126/science.1076093
Date:
09-Jul-02     Release date:   12-Oct-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A
Seq:
Struc:
282 a.a.
92 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nuclear mRNA splicing, via spliceosome   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1126/science.1076093 Science 298:1421-1424 (2002)
PubMed id: 12376595  
 
 
Transition state stabilization by a catalytic RNA.
P.B.Rupert, A.P.Massey, S.T.Sigurdsson, A.R.Ferré-D'Amaré.
 
  ABSTRACT  
 
The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Comparison of the active sites of precursor, transition state mimic, and product structures. (A) Omit |F[o]| - |F[c]| map (3 SD) of the precursor, trapped by replacing the 2'-OH nucleophile with a methoxy group (5). Arrows and mesh are as in Fig. 1. (B) Omit |F[o]| - |F[c]| map (3 SD) of the ribozyme-product complex. (C) Superposition of the precursor (black) and vanadate models. (D) Superposition of product (black) and vanadate models. Within experimental error (Table 1), the active site is rigid (16).
Figure 3.
Fig. 3. Summary of active site hydrogen bonds (6). (A) Precursor complex stabilized by two hydrogen bonds (dashed lines) from G8. (B) Transition state mimic complex stabilized by five hydrogen bonds. (The green triangle connects the equatorial oxygens of the vanadate.) Although modification interference studies found no evidence that N1 of A38 is protonated (25), full time courses were not examined by those authors. Protonation is inferred from the distance between N1 of A38 and the 5'-oxygen (6). (C) Product complex stabilized by three hydrogen bonds. The hydrogen bond between N1 of A38 and the 5'-OH of G+1 would orient the latter for the ligation reaction.
 
  The above figures are reprinted by permission from the AAAs: Science (2002, 298, 1421-1424) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21428954 D.M.Lilley (2011).
Catalysis by the nucleolytic ribozymes.
  Biochem Soc Trans, 39, 641-646.  
21857665 D.M.Shechner, and D.P.Bartel (2011).
The structural basis of RNA-catalyzed RNA polymerization.
  Nat Struct Mol Biol, 18, 1036-1042.
PDB codes: 3r1h 3r1l
21199369 I.Drude, A.Strahl, D.Galla, O.Müller, and S.Müller (2011).
Design of hairpin ribozyme variants with improved activity for poorly processed substrates.
  FEBS J, 278, 622-633.  
21138969 I.V.Novikova, B.H.Hassan, M.G.Mirzoyan, and N.B.Leontis (2011).
Engineering cooperative tecto-RNA complexes having programmable stoichiometries.
  Nucleic Acids Res, 39, 2903-2917.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20822574 A.R.Ferré-D'Amaré (2010).
The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.
  Q Rev Biophys, 43, 423-447.  
20554048 A.R.Ferré-D'Amaré (2010).
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
  Methods, 52, 159-167.  
20689681 N.B.Ulyanov, and T.L.James (2010).
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA.
  New J Chem, 34, 910-917.  
20547881 T.J.Wilson, N.S.Li, J.Lu, J.K.Frederiksen, J.A.Piccirilli, and D.M.Lilley (2010).
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.
  Proc Natl Acad Sci U S A, 107, 11751-11756.  
20080629 X.Zuo, J.Wang, P.Yu, D.Eyler, H.Xu, M.R.Starich, D.M.Tiede, A.E.Simon, W.Kasprzak, C.D.Schwieters, B.A.Shapiro, and Y.X.Wang (2010).
Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus.
  Proc Natl Acad Sci U S A, 107, 1385-1390.
PDB code: 2krl
19528080 C.L.Zirbel, J.E.Sponer, J.Sponer, J.Stombaugh, and N.B.Leontis (2009).
Classification and energetics of the base-phosphate interactions in RNA.
  Nucleic Acids Res, 37, 4898-4918.  
19623596 J.Buck, Y.L.Li, C.Richter, J.Vergne, M.C.Maurel, and H.Schwalbe (2009).
NMR spectroscopic characterization of the adenine-dependent hairpin ribozyme.
  Chembiochem, 10, 2100-2110.  
19330013 L.Liu, J.W.Cottrell, L.G.Scott, and M.J.Fedor (2009).
Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme.
  Nat Chem Biol, 5, 351-357.  
19223444 M.A.Ditzler, J.Sponer, and N.G.Walter (2009).
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
  RNA, 15, 560-575.  
19702306 M.Guo, R.C.Spitale, R.Volpini, J.Krucinska, G.Cristalli, P.R.Carey, and J.E.Wedekind (2009).
Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.
  J Am Chem Soc, 131, 12908-12909.  
19416070 M.J.Fedor (2009).
Comparative enzymology and structural biology of RNA self-cleavage.
  Annu Rev Biophys, 38, 271-299.  
19476496 M.Ztouti, H.Kaddour, F.Miralles, C.Simian, J.Vergne, G.Hervé, and M.C.Maurel (2009).
Adenine, a hairpin ribozyme cofactor - high-pressure and competition studies.
  FEBS J, 276, 2574-2588.  
19398008 P.Banás, P.Jurecka, N.G.Walter, J.Sponer, and M.Otyepka (2009).
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
  Methods, 49, 202-216.  
19559088 R.C.Spitale, and J.E.Wedekind (2009).
Exploring ribozyme conformational changes with X-ray crystallography.
  Methods, 49, 87.  
19354216 R.C.Spitale, R.Volpini, M.G.Heller, J.Krucinska, G.Cristalli, and J.E.Wedekind (2009).
Identification of an imino group indispensable for cleavage by a small ribozyme.
  J Am Chem Soc, 131, 6093-6095.
PDB codes: 3gs1 3gs5 3gs8
19634899 R.C.Spitale, R.Volpini, M.V.Mungillo, J.Krucinska, G.Cristalli, and J.E.Wedekind (2009).
Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.
  Biochemistry, 48, 7777-7779.
PDB codes: 3i2q 3i2r 3i2s 3i2u
19054068 Y.L.Li, J.Vergne, C.Torchet, and M.C.Maurel (2009).
In vitro selection of adenine-dependent ribozyme against Tpl2/Cot oncogene.
  FEBS J, 276, 303-314.  
18423397 A.T.Torelli, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2008).
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
  Biochem Biophys Res Commun, 371, 154-158.
PDB code: 3cqs
18636557 A.Vourekas, V.Stamatopoulou, C.Toumpeki, M.Tsitlaidou, and D.Drainas (2008).
Insights into functional modulation of catalytic RNA activity.
  IUBMB Life, 60, 669-683.  
18729108 B.Lippert (2008).
Ligand-pKa shifts through metals: potential relevance to ribozyme chemistry.
  Chem Biodivers, 5, 1455-1474.  
18596253 C.MacElrevey, J.D.Salter, J.Krucinska, and J.E.Wedekind (2008).
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
  RNA, 14, 1600-1616.
PDB codes: 3b58 3b5a 3b5f 3b5s 3b91 3bbi 3bbk 3bbm 3cr1
17910059 J.J.Ellis, and S.Jones (2008).
Evaluating conformational changes in protein structures binding RNA.
  Proteins, 70, 1518-1526.  
18566190 K.Nam, J.Gao, and D.M.York (2008).
Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases.
  RNA, 14, 1501-1507.  
18345664 K.Nam, J.Gao, and D.M.York (2008).
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.
  J Am Chem Soc, 130, 4680-4691.  
18988629 M.A.Ditzler, D.Rueda, J.Mo, K.Håkansson, and N.G.Walter (2008).
A rugged free energy landscape separates multiple functional RNA folds throughout denaturation.
  Nucleic Acids Res, 36, 7088-7099.  
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
17957392 S.A.Gabel, and R.E.London (2008).
Ternary borate-nucleoside complex stabilization by ribonuclease A demonstrates phosphate mimicry.
  J Biol Inorg Chem, 13, 207-217.  
17998292 S.Gaur, J.E.Heckman, and J.M.Burke (2008).
Mutational inhibition of ligation in the hairpin ribozyme: substitutions of conserved nucleobases A9 and A10 destabilize tertiary structure and selectively promote cleavage.
  RNA, 14, 55-65.  
18834200 Y.I.Chi, M.Martick, M.Lares, R.Kim, W.G.Scott, and S.H.Kim (2008).
Capturing hammerhead ribozyme structures in action by modulating general base catalysis.
  PLoS Biol, 6, e234.
PDB codes: 2qus 2quw
17846637 A.Serganov, and D.J.Patel (2007).
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.
  Nat Rev Genet, 8, 776-790.  
17488874 A.T.Torelli, J.Krucinska, and J.E.Wedekind (2007).
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
  RNA, 13, 1052-1070.
PDB codes: 2p7d 2p7e 2p7f
17582172 C.MacElrevey, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2007).
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
  Acta Crystallogr D Biol Crystallogr, 63, 812-825.
PDB codes: 2npy 2npz
17570822 D.M.Lilley (2007).
A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes.
  Biol Chem, 388, 699-704.  
17186477 E.Mayaan, A.Moser, A.D.MacKerell, and D.M.York (2007).
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.
  J Comput Chem, 28, 495-507.  
18081104 H.Linjalahti, and S.Mikkola (2007).
Intra- and intermolecular interactions influence the reactivity of RNA oligonucleotides.
  Chem Biodivers, 4, 2938-2947.  
17685395 M.A.Ditzler, E.A.Alemán, D.Rueda, and N.G.Walter (2007).
Focus on function: single molecule RNA enzymology.
  Biopolymers, 87, 302-316.  
18158891 N.G.Walter (2007).
Ribozyme catalysis revisited: is water involved?
  Mol Cell, 28, 923-929.  
17391549 P.C.Bevilacqua, A.L.Cerrone-Szakal, and N.A.Siegfried (2007).
Insight into the functional versatility of RNA through model-making with applications to data fitting.
  Q Rev Biophys, 40, 55-85.  
17981494 S.A.Strobel, and J.C.Cochrane (2007).
RNA catalysis: ribozymes, ribosomes, and riboswitches.
  Curr Opin Chem Biol, 11, 636-643.  
17496145 S.Liu, G.Bokinsky, N.G.Walter, and X.Zhuang (2007).
Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".
  Proc Natl Acad Sci U S A, 104, 12634-12639.  
17574837 T.E.Edwards, D.J.Klein, and A.R.Ferré-D'Amaré (2007).
Riboswitches: small-molecule recognition by gene regulatory RNAs.
  Curr Opin Struct Biol, 17, 273-279.  
17464286 T.J.Wilson, A.C.McLeod, and D.M.Lilley (2007).
A guanine nucleobase important for catalysis by the VS ribozyme.
  EMBO J, 26, 2489-2500.  
16411759 D.Lambert, J.E.Heckman, and J.M.Burke (2006).
Cation-specific structural accommodation within a catalytic RNA.
  Biochemistry, 45, 829-838.  
16411744 J.Salter, J.Krucinska, S.Alam, V.Grum-Tokars, and J.E.Wedekind (2006).
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.
  Biochemistry, 45, 686-700.
PDB codes: 1zfr 1zft 1zfv 1zfx 2bcy 2bcz 2fgp 2oue
16938834 M.M.Rhodes, K.Réblová, J.Sponer, and N.G.Walter (2006).
Trapped water molecules are essential to structural dynamics and function of a ribozyme.
  Proc Natl Acad Sci U S A, 103, 13380-13385.  
16859740 M.Martick, and W.G.Scott (2006).
Tertiary contacts distant from the active site prime a ribozyme for catalysis.
  Cell, 126, 309-320.
PDB codes: 2goz 3zd5
16601679 M.Nowotny, and W.Yang (2006).
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.
  EMBO J, 25, 1924-1933.
PDB codes: 2g8f 2g8h 2g8i 2g8k 2g8u 2g8v 2g8w
16601203 T.J.Wilson, J.Ouellet, Z.Y.Zhao, S.Harusawa, L.Araki, T.Kurihara, and D.M.Lilley (2006).
Nucleobase catalysis in the hairpin ribozyme.
  RNA, 12, 980-987.  
16100266 A.W.Van Wynsberghe, and Q.Cui (2005).
Comparison of mode analyses at different resolutions applied to nucleic acid systems.
  Biophys J, 89, 2939-2949.  
16240045 C.Marian, D.Nolting, and R.Weinkauf (2005).
The electronic spectrum of protonated adenine: theory and experiment.
  Phys Chem Chem Phys, 7, 3306-3316.  
15919196 D.M.Lilley (2005).
Structure, folding and mechanisms of ribozymes.
  Curr Opin Struct Biol, 15, 313-323.  
15870731 J.A.Doudna, and J.R.Lorsch (2005).
Ribozyme catalysis: not different, just worse.
  Nat Struct Mol Biol, 12, 395-402.  
16408062 J.A.Doudna (2005).
Chemical biology at the crossroads of molecular structure and mechanism.
  Nat Chem Biol, 1, 300-303.  
15744318 J.N.Pitt, and A.R.Ferré-D'Amaré (2005).
How RNA closes a Diel.
  Nat Struct Mol Biol, 12, 206-208.  
15956979 M.J.Fedor, and J.R.Williamson (2005).
The catalytic diversity of RNAs.
  Nat Rev Mol Cell Biol, 6, 399-412.  
16128815 S.A.Ivanov, S.Vauléon, and S.Müller (2005).
Efficient RNA ligation by reverse-joined hairpin ribozymes and engineering of twin ribozymes consisting of conventional and reverse-joined hairpin ribozyme units.
  FEBS J, 272, 4464-4474.  
16407993 S.R.Das, and J.A.Piccirilli (2005).
General acid catalysis by the hepatitis delta virus ribozyme.
  Nat Chem Biol, 1, 45-52.  
16242990 S.R.Das, R.Fong, and J.A.Piccirilli (2005).
Nucleotide analogues to investigate RNA structure and function.
  Curr Opin Chem Biol, 9, 585-593.  
15870387 S.Tobé, T.Heams, J.Vergne, G.Hervé, and M.C.Maurel (2005).
The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure.
  Nucleic Acids Res, 33, 2557-2564.  
16298301 T.J.McCarthy, M.A.Plog, S.A.Floy, J.A.Jansen, J.K.Soukup, and G.A.Soukup (2005).
Ligand requirements for glmS ribozyme self-cleavage.
  Chem Biol, 12, 1221-1226.  
15141216 A.Ke, K.Zhou, F.Ding, J.H.Cate, and J.A.Doudna (2004).
A conformational switch controls hepatitis delta virus ribozyme catalysis.
  Nature, 429, 201-205.
PDB codes: 1sj3 1sj4 1sjf 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1vc7
15064361 A.P.Massey, and S.T.Sigurdsson (2004).
Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme.
  Nucleic Acids Res, 32, 2017-2022.  
14691941 A.R.Ferré-D'Amaré (2004).
The hairpin ribozyme.
  Biopolymers, 73, 71-78.  
14730013 D.M.Lilley (2004).
The Varkud satellite ribozyme.
  RNA, 10, 151-158.  
15218105 D.Rueda, G.Bokinsky, M.M.Rhodes, M.J.Rust, X.Zhuang, and N.G.Walter (2004).
Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance.
  Proc Natl Acad Sci U S A, 101, 10066-10071.  
15525509 F.Guo, A.R.Gooding, and T.R.Cech (2004).
Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site.
  Mol Cell, 16, 351-362.
PDB code: 1x8w
15324800 M.Egli (2004).
"Deoxyribo nanonucleic acid"; antiparallel, parallel, and unparalleled.
  Chem Biol, 11, 1027-1029.  
15556400 M.Egli (2004).
Nucleic acid crystallography: current progress.
  Curr Opin Chem Biol, 8, 580-591.  
15475966 M.K.Nahas, T.J.Wilson, S.Hohng, K.Jarvie, D.M.Lilley, and T.Ha (2004).
Observation of internal cleavage and ligation reactions of a ribozyme.
  Nat Struct Mol Biol, 11, 1107-1113.  
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
14691943 P.C.Bevilacqua, T.S.Brown, S.Nakano, and R.Yajima (2004).
Catalytic roles for proton transfer and protonation in ribozymes.
  Biopolymers, 73, 90.  
13678961 D.M.Lilley (2003).
The origins of RNA catalysis in ribozymes.
  Trends Biochem Sci, 28, 495-501.  
12618186 D.R.Davies, H.Interthal, J.J.Champoux, and W.G.Hol (2003).
Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.
  Chem Biol, 10, 139-147.
PDB code: 1nop
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
14532128 M.De la Peña, S.Gago, and R.Flores (2003).
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity.
  EMBO J, 22, 5561-5570.  
12876372 P.B.Rupert, H.Xiao, and A.R.Ferré-D'Amaré (2003).
U1A RNA-binding domain at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 1521-1524.
PDB code: 1nu4
14668444 P.J.Unrau, and D.P.Bartel (2003).
An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects.
  Proc Natl Acad Sci U S A, 100, 15393-15397.  
12914783 S.S.Martin, S.Wachi, and E.P.Baldwin (2003).
Vanadate-based transition-state analog inhibitors of Cre-LoxP recombination.
  Biochem Biophys Res Commun, 308, 529-534.  
14654688 Y.Pan, and A.D.MacKerell (2003).
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.
  Nucleic Acids Res, 31, 7131-7140.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.