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PDBsum entry 2aas

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protein links
Hydrolase(endoribonuclease) PDB id
2aas
Jmol
Contents
Protein chain
124 a.a. *
* Residue conservation analysis
PDB id:
2aas
Name: Hydrolase(endoribonuclease)
Title: High-resolution three-dimensional structure of ribonuclease a in solution by nuclear magnetic resonance spectroscopy
Structure: Ribonuclease a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
NMR struc: 32 models
Authors: J.Santoro,C.Gonzalez,M.Bruix,J.L.Neira,J.L.Nieto,J.Herranz, M.Rico
Key ref: J.Santoro et al. (1993). High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy. J Mol Biol, 229, 722-734. PubMed id: 8381876
Date:
20-Nov-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     6 terms  

 

 
J Mol Biol 229:722-734 (1993)
PubMed id: 8381876  
 
 
High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy.
J.Santoro, C.González, M.Bruix, J.L.Neira, J.L.Nieto, J.Herranz, M.Rico.
 
  ABSTRACT  
 
High-resolution three-dimensional structures of bovine pancreatic ribonuclease A in aqueous solution have been determined by nuclear magnetic resonance (NMR) spectroscopy combined with restrained molecular dynamics calculations. The structures are based on: (1) 464 interproton distance constraints with accurate upper and lower limits, determined from build-up rates of nuclear Overhauser effects (NOE) by using the complete relaxation matrix; (2) 999 more approximate upper limits for interproton distances; and (3) 42 dihedral angle constraints (37 for phi and 5 for chi 1). A total of 16 structures were calculated, which show a root-mean-square (r.m.s.) deviation of 0.66 A for the backbone atoms and 1.68 A for all heavy-atoms. The converged structures are highly similar to those found in the crystal state. r.m.s. deviation of backbone atom positions in the crystal as compared to those in the average solution structure is 0.92 A. Observed differences are concentrated in loop regions and in the neighborhood of His119 and His48 side-chains. Dynamic aspects, such as H/D amide proton exchange and side-chain mobility have been examined.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20423719 S.Dubey, and Y.N.Kalia (2010).
Non-invasive iontophoretic delivery of enzymatically active ribonuclease A (13.6 kDa) across intact porcine and human skins.
  J Control Release, 145, 203-209.  
19189375 D.V.Laurents, M.Bruix, M.A.Jiménez, J.Santoro, E.Boix, M.Moussaoui, M.V.Nogués, and M.Rico (2009).
The (1)H, (13)C, (15)N resonance assignment, solution structure, and residue level stability of eosinophil cationic protein/RNase 3 determined by NMR spectroscopy.
  Biopolymers, 91, 1018-1028.
PDB code: 2kb5
19436956 I.J.Day, K.Maeda, H.J.Paisley, K.H.Mok, and P.J.Hore (2009).
Refolding of ribonuclease A monitored by real-time photo-CIDNP NMR spectroscopy.
  J Biomol NMR, 44, 77-86.  
19373927 R.Vilà, A.Benito, M.Ribó, and M.Vilanova (2009).
Mapping the stability clusters in bovine pancreatic ribonuclease A.
  Biopolymers, 91, 1038-1047.  
18588487 B.S.Mamathambika, and J.C.Bardwell (2008).
Disulfide-linked protein folding pathways.
  Annu Rev Cell Dev Biol, 24, 211-235.  
18161991 E.D.Merkley, B.Bernard, and V.Daggett (2008).
Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A.
  Biochemistry, 47, 880-892.  
18192347 M.Bruix, M.Ribó, A.Benito, D.V.Laurents, M.Rico, and M.Vilanova (2008).
Destabilizing mutations alter the hydrogen exchange mechanism in ribonuclease A.
  Biophys J, 94, 2297-2305.  
17141728 J.W.Brock, J.M.Ames, S.R.Thorpe, and J.W.Baynes (2007).
Formation of methionine sulfoxide during glycoxidation and lipoxidation of ribonuclease A.
  Arch Biochem Biophys, 457, 170-176.  
17384067 M.Noronha, J.C.Lima, E.Paci, H.Santos, and A.L.Maçanita (2007).
Tracking local conformational changes of ribonuclease A using picosecond time-resolved fluorescence of the six tyrosine residues.
  Biophys J, 92, 4401-4414.  
16542150 J.Font, A.Benito, J.Torrent, R.Lange, M.Ribó, and M.Vilanova (2006).
Pressure- and temperature-induced unfolding studies: thermodynamics of core hydrophobicity and packing of ribonuclease A.
  Biol Chem, 387, 285-296.  
16798802 J.Font, J.Torrent, M.Ribó, D.V.Laurents, C.Balny, M.Vilanova, and R.Lange (2006).
Pressure-jump-induced kinetics reveals a hydration dependent folding/unfolding mechanism of ribonuclease A.
  Biophys J, 91, 2264-2274.  
16415350 J.P.López-Alonso, M.Bruix, J.Font, M.Ribó, M.Vilanova, M.Rico, G.Gotte, M.Libonati, C.González, and D.V.Laurents (2006).
Formation, structure, and dissociation of the ribonuclease S three-dimensional domain-swapped dimer.
  J Biol Chem, 281, 9400-9406.  
17129156 M.M.Somoza, V.V.Ponkratov, and J.Friedrich (2006).
Investigation of spectral diffusion in ribonuclease by photolabeling of intrinsic aromatic amino acids.
  J Chem Phys, 125, 194713.  
16791739 N.Powers, and J.H.Jensen (2006).
Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.
  J Biomol NMR, 35, 39-51.  
16415060 Y.B.Yan, J.Zhang, H.W.He, and H.M.Zhou (2006).
Oligomerization and aggregation of bovine pancreatic ribonuclease A: characteristic events observed by FTIR spectroscopy.
  Biophys J, 90, 2525-2533.  
15908578 A.Caballero-Herrera, K.Nordstrand, K.D.Berndt, and L.Nilsson (2005).
Effect of urea on peptide conformation in water: molecular dynamics and experimental characterization.
  Biophys J, 89, 842-857.  
15861139 C.Ritter, K.Quirin, M.Kowarik, and A.Helenius (2005).
Minor folding defects trigger local modification of glycoproteins by the ER folding sensor GT.
  EMBO J, 24, 1730-1738.  
16199662 D.A.Schultz, A.M.Friedman, M.A.White, and R.O.Fox (2005).
The crystal structure of the cis-proline to glycine variant (P114G) of ribonuclease A.
  Protein Sci, 14, 2862-2870.
PDB code: 1kh8
16335788 D.Gaur, and J.K.Batra (2005).
Role of aspartic acid 121 in human pancreatic ribonuclease catalysis.
  Mol Cell Biochem, 275, 95.  
16237662 O.T.Akinsiku, E.T.Yu, and D.Fabris (2005).
Mass spectrometric investigation of protein alkylation by the RNA footprinting probe kethoxal.
  J Mass Spectrom, 40, 1372-1381.  
15041676 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2004).
Dynamic properties of the N-terminal swapped dimer of ribonuclease A.
  Biophys J, 86, 2383-2391.  
14990499 C.L.Teng, and R.G.Bryant (2004).
Mapping oxygen accessibility to ribonuclease a using high-resolution NMR relaxation spectroscopy.
  Biophys J, 86, 1713-1725.  
15479244 J.Köditz, R.Ulbrich-Hofmann, and U.Arnold (2004).
Probing the unfolding region of ribonuclease A by site-directed mutagenesis.
  Eur J Biochem, 271, 4147-4156.  
12945053 A.Merlino, L.Vitagliano, M.A.Ceruso, and L.Mazzarella (2003).
Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin.
  Proteins, 53, 101-110.  
12557184 C.González, J.L.Neira, S.Ventura, S.Bronsoms, M.Rico, and F.X.Avilés (2003).
Structure and dynamics of the potato carboxypeptidase inhibitor by 1H and 15N NMR.
  Proteins, 50, 410-422.
PDB code: 1h20
12382288 A.Merlino, L.Vitagliano, M.A.Ceruso, A.Di Nola, and L.Mazzarella (2002).
Global and local motions in ribonuclease A: a molecular dynamics study.
  Biopolymers, 65, 274-283.  
12153580 J.Köditz, U.Arnold, and R.Ulbrich-Hofmann (2002).
Dissecting the effect of trifluoroethanol on ribonuclease A. Subtle structural changes detected by nonspecific proteases.
  Eur J Biochem, 269, 3831-3837.  
11746706 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2002).
Reversible substrate-induced domain motions in ribonuclease A.
  Proteins, 46, 97.
PDB codes: 1jvt 1jvu 1jvv
11856829 R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, and L.Mazzarella (2002).
Atomic resolution structures of ribonuclease A at six pH values.
  Acta Crystallogr D Biol Crystallogr, 58, 441-450.
PDB codes: 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8
12324397 R.E.Georgescu, E.G.Alexov, and M.R.Gunner (2002).
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins.
  Biophys J, 83, 1731-1748.  
11514676 A.T.Alexandrescu, D.R.Snyder, and F.Abildgaard (2001).
NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths.
  Protein Sci, 10, 1856-1868.  
11288180 B.Das, and H.Meirovitch (2001).
Optimization of solvation models for predicting the structure of surface loops in proteins.
  Proteins, 43, 303-314.  
11316877 S.D.Stelea, P.Pancoska, A.S.Benight, and T.A.Keiderling (2001).
Thermal unfolding of ribonuclease A in phosphate at neutral pH: deviations from the two-state model.
  Protein Sci, 10, 970-978.  
11180053 S.Takashima (2001).
The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.
  Biopolymers, 58, 398-409.  
11316874 V.A.Jaravine, A.T.Alexandrescu, and S.Grzesiek (2001).
Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide.
  Protein Sci, 10, 943-950.  
11266618 Y.B.Yan, B.Jiang, R.Q.Zhang, and H.M.Zhou (2001).
Two-phase unfolding pathway of ribonuclease A during denaturation induced by dithiothreitol.
  Protein Sci, 10, 321-328.  
11582573 S.Capasso, and P.Di Cerbo (2000).
Formation of an RNase A derivative containing an aminosuccinyl residue in place of asparagine 67.
  Biopolymers, 56, 14-19.  
10393919 G.Chakshusmathi, G.S.Ratnaparkhi, P.K.Madhu, and R.Varadarajan (1999).
Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments.
  Proc Natl Acad Sci U S A, 96, 7899-7904.  
10563503 S.Capasso, and S.Salvadori (1999).
Effect of the three-dimensional structure on the deamidation reaction of ribonuclease A.
  J Pept Res, 54, 377-382.  
10089510 C.Sadasivan, H.G.Nagendra, and M.Vijayan (1998).
Plasticity, hydration and accessibility in ribonuclease A. The structure of a new crystal form and its low-humidity variant.
  Acta Crystallogr D Biol Crystallogr, 54, 1343-1352.
PDB codes: 1xps 1xpt
9649343 V.P.Denisov, and B.Halle (1998).
Thermal denaturation of ribonuclease A characterized by water 17O and 2H magnetic relaxation dispersion.
  Biochemistry, 37, 9595-9604.  
9254610 D.Juminaga, W.J.Wedemeyer, R.Garduño-Júarez, M.A.McDonald, and H.A.Scheraga (1997).
Tyrosyl interactions in the folding and unfolding of bovine pancreatic ribonuclease A: a study of tyrosine-to-phenylalanine mutants.
  Biochemistry, 36, 10131-10145.  
  9260280 F.Catanzano, G.Graziano, S.Capasso, and G.Barone (1997).
Thermodynamic analysis of the effect of selective monodeamidation at asparagine 67 in ribonuclease A.
  Protein Sci, 6, 1682-1693.  
9057494 G.Kurapkat, P.Krüger, A.Wollmer, J.Fleischhauer, B.Kramer, E.Zobel, A.Koslowski, H.Botterweck, and R.W.Woody (1997).
Calculations of the CD spectrum of bovine pancreatic ribonuclease.
  Biopolymers, 41, 267-287.  
9335525 J.H.Laity, C.C.Lester, S.Shimotakahara, D.E.Zimmerman, G.T.Montelione, and H.A.Scheraga (1997).
Structural characterization of an analog of the major rate-determining disulfide folding intermediate of bovine pancreatic ribonuclease A.
  Biochemistry, 36, 12683-12699.  
9461294 O.Lequin, H.Thüring, M.Robin, and J.Y.Lallemand (1997).
Three-dimensional solution structure of human angiogenin determined by 1H,15N-NMR spectroscopy--characterization of histidine protonation states and pKa values.
  Eur J Biochem, 250, 712-726.
PDB code: 1awz
  9098896 P.Polverino de Laureto, E.Scaramella, V.De Filippis, M.Bruix, M.Rico, and A.Fontana (1997).
Limited proteolysis of ribonuclease A with thermolysin in trifluoroethanol.
  Protein Sci, 6, 860-872.  
9174359 S.Padmanabhan, M.A.Jiménez, C.Gonzalez, J.M.Sanz, G.Giménez-Gallego, and M.Rico (1997).
Three-dimensional solution structure and stability of phage 434 Cro protein.
  Biochemistry, 36, 6424-6436.
PDB code: 1zug
9188686 S.Shimotakahara, C.B.Rios, J.H.Laity, D.E.Zimmerman, H.A.Scheraga, and G.T.Montelione (1997).
NMR structural analysis of an analog of an intermediate formed in the rate-determining step of one pathway in the oxidative folding of bovine pancreatic ribonuclease A: automated analysis of 1H, 13C, and 15N resonance assignments for wild-type and [C65S, C72S] mutant forms.
  Biochemistry, 36, 6915-6929.  
  8844852 C.Toiron, C.González, M.Bruix, and M.Rico (1996).
Three-dimensional structure of the complexes of ribonuclease A with 2',5'-CpA and 3',5'-d(CpA) in aqueous solution, as obtained by NMR and restrained molecular dynamics.
  Protein Sci, 5, 1633-1647.  
  8897611 G.Nadig, G.S.Ratnaparkhi, R.Varadarajan, and S.Vishveshwara (1996).
Dynamics of ribonuclease A and ribonuclease S: computational and experimental studies.
  Protein Sci, 5, 2104-2114.  
8672483 J.Antosiewicz, J.A.McCammon, and M.K.Gilson (1996).
The determinants of pKas in proteins.
  Biochemistry, 35, 7819-7833.  
8688423 O.Lequin, C.Albaret, F.Bontems, G.Spik, and J.Y.Lallemand (1996).
Solution structure of bovine angiogenin by 1H nuclear magnetic resonance spectroscopy.
  Biochemistry, 35, 8870-8880.
PDB code: 1gio
8700871 S.N.Loh, C.A.Rohl, T.Kiefhaber, and R.L.Baldwin (1996).
A general two-process model describes the hydrogen exchange behavior of RNase A in unfolding conditions.
  Proc Natl Acad Sci U S A, 93, 1982-1987.  
8608120 T.N.Jaishree, V.Ramakrishnan, and S.W.White (1996).
Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy.
  Biochemistry, 35, 2845-2853.  
8756476 W.A.Houry, D.M.Rothwarf, and H.A.Scheraga (1996).
Circular dichroism evidence for the presence of burst-phase intermediates on the conformational folding pathway of ribonuclease A.
  Biochemistry, 35, 10125-10133.  
8794754 W.A.Houry, and H.A.Scheraga (1996).
Structure of a hydrophobically collapsed intermediate on the conformational folding pathway of ribonuclease A probed by hydrogen-deuterium exchange.
  Biochemistry, 35, 11734-11746.  
7744072 A.D'Ursi, H.Oschkinat, C.Cieslar, D.Picone, G.D'Alessio, P.Amodeo, and P.A.Temussi (1995).
Assignment and secondary-structure determination of monomeric bovine seminal ribonuclease employing computer-assisted evaluation of homonuclear three-dimensional 1H-NMR spectra.
  Eur J Biochem, 229, 494-502.  
7925406 C.Reisdorf, D.Abergel, F.Bontems, J.Y.Lallemand, J.P.Decottignies, and G.Spik (1994).
Proton resonance assignments and secondary structure of bovine angiogenin.
  Eur J Biochem, 224, 811-822.  
  7756988 I.Zegers, D.Maes, M.H.Dao-Thi, F.Poortmans, R.Palmer, and L.Wyns (1994).
The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.
  Protein Sci, 3, 2322-2339.
PDB codes: 1rpf 1rpg 1rph
  7920260 M.J.Scanlon, and R.S.Norton (1994).
Multiple conformations of the sea anemone polypeptide anthopleurin-A in solution.
  Protein Sci, 3, 1121-1124.  
7919003 T.D.Veenstra, and L.Lee (1994).
NMR study of the positions of His-12 and His-119 in the ribonuclease A-uridine vanadate complex.
  Biophys J, 67, 331-335.  
  8003961 U.Neumann, and J.Hofsteenge (1994).
Interaction of semisynthetic variants of RNase A with ribonuclease inhibitor.
  Protein Sci, 3, 248-256.  
  8142897 V.S.deMel, M.S.Doscher, M.A.Glinn, P.D.Martin, M.L.Ram, and B.F.Edwards (1994).
Structural investigation of catalytically modified F120L and F120Y semisynthetic ribonucleases.
  Protein Sci, 3, 39-50.
PDB codes: 1ssa 1ssb
8243469 H.C.Joao, and R.A.Dwek (1993).
Effects of glycosylation on protein structure and dynamics in ribonuclease B and some of its individual glycoforms.
  Eur J Biochem, 218, 239-244.  
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 code is shown on the right.