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PDBsum entry 1rcn

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protein dna_rna links
Hydrolase/DNA PDB id
1rcn
Jmol
Contents
Protein chain
124 a.a. *
DNA/RNA
Waters ×68
* Residue conservation analysis
PDB id:
1rcn
Name: Hydrolase/DNA
Title: Crystal structure of the ribonuclease a d(aptpapapg) complex : direct evidence for extended substrate recognition
Structure: DNA (5'-d( Ap Tp Ap A)-3'). Chain: d. Engineered: yes. Protein (ribonuclease a . Chain: e. Ec: 3.1.27.5
Source: Synthetic: yes. Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Secretion: milk
Resolution:
2.32Å     R-factor:   0.172    
Authors: J.C.Fontecilla-Camps,R.De Llorens,M.H.Le Du,C.M.Cuchillo
Key ref: J.C.Fontecilla-Camps et al. (1994). Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition. J Biol Chem, 269, 21526-21531. PubMed id: 8063789
Date:
27-May-94     Release date:   30-Sep-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     7 terms  

 

 
J Biol Chem 269:21526-21531 (1994)
PubMed id: 8063789  
 
 
Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition.
J.C.Fontecilla-Camps, R.de Llorens, M.H.le Du, C.M.Cuchillo.
 
  ABSTRACT  
 
The crystal structure of the complex between ribonuclease A and d(ApTpApApG) has been solved by x-ray crystallography using the molecular replacement method. The model includes, besides the enzyme, the d(ApTpApA) 5'-segment (A1T2A3A4) and 68 solvent molecules. The R-factor for the strongest 87% of the measured data that partially extends to 2.3-A resolution is 0.207. The A1 position is well defined; the 5'-O of the deoxyribose establishes a hydrogen bond with a solvent molecule that is, in turn, bonded to the epsilon-amino group of Lys66. The base (B0 site) is well ordered; it interacts with a symmetry-related enzyme molecule. In the crystal, the phosphate group at the p0 site has no direct charge compensation. However, Lys66 is not too far, and, in solution, it could bind to it. The T2 (R1B1p1) site is occupied as in other complex structures, and it is defined by very good electron density. The A3 site shows that the adenine moiety interacts with Asn71 and Gln69 and that the phosphate at p2 forms a salt bridge with Lys7. The most consistent model for the base of A4 (B3), both in terms of electron density and stereochemistry, shows that it forms a hydrogen bond with Gln69 and a g-g- array with the base at B2. The stacking of B2 and B3 may be a general feature of the binding of polyribonucleotides to ribonuclease A. The side chains of Gln69, Asn71, and Glu111 may thus constitute a malleable binding site capable of establishing various hydrogen bonds depending on the nature of the stacked bases. There is no evidence for the 3' G5 site in the electron density map.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205197 N.Thiyagarajan, B.D.Smith, R.T.Raines, and K.R.Acharya (2011).
Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A.
  FEBS J, 278, 541-549.
PDB codes: 2xog 2xoi
19191310 D.E.Holloway, G.B.Chavali, D.D.Leonidas, M.D.Baker, and K.R.Acharya (2009).
Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: An X-ray crystallographic study.
  Biopolymers, 91, 995.
PDB codes: 2w5g 2w5i 2w5k 2w5l 2w5m
19090717 D.Sikriwal, D.Seth, and J.K.Batra (2009).
Role of catalytic and non-catalytic subsite residues in ribonuclease activity of human eosinophil-derived neurotoxin.
  Biol Chem, 390, 225-234.  
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
18001769 J.E.Lee, E.Bae, C.A.Bingman, G.N.Phillips, and R.T.Raines (2008).
Structural basis for catalysis by onconase.
  J Mol Biol, 375, 165-177.
PDB codes: 2gmk 2i5s
18474529 O.A.Zasedateleva, A.L.Mikheikin, A.Y.Turygin, D.V.Prokopenko, A.V.Chudinov, E.E.Belobritskaya, V.R.Chechetkin, and A.S.Zasedatelev (2008).
Gel-based oligonucleotide microarray approach to analyze protein-ssDNA binding specificity.
  Nucleic Acids Res, 36, e61.  
18268334 Z.Du, J.K.Lee, R.Tjhen, R.M.Stroud, and T.L.James (2008).
Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage.
  Proc Natl Acad Sci U S A, 105, 2391-2396.
PDB codes: 3c4b 3c4t
17192592 M.Moussaoui, C.M.Cuchillo, and M.V.Nogués (2007).
A phosphate-binding subsite in bovine pancreatic ribonuclease A can be converted into a very efficient catalytic site.
  Protein Sci, 16, 99.  
  17768339 S.B.Larson, J.S.Day, R.Cudney, and A.McPherson (2007).
A new crystal form of bovine pancreatic RNase A in complex with 2'-deoxyguanosine-5'-monophosphate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 728-733.
PDB code: 2qca
17417947 S.S.Pachouri, R.C.Sobti, P.Kaur, and J.Singh (2007).
Contrasting impact of DNA repair gene XRCC1 polymorphisms Arg399Gln and Arg194Trp on the risk of lung cancer in the north-Indian population.
  DNA Cell Biol, 26, 186-191.  
16730994 D.D.Leonidas, T.K.Maiti, A.Samanta, S.Dasgupta, T.Pathak, S.E.Zographos, and N.G.Oikonomakos (2006).
The binding of 3'-N-piperidine-4-carboxyl-3'-deoxy-ara-uridine to ribonuclease A in the crystal.
  Bioorg Med Chem, 14, 6055-6064.
PDB codes: 2g8q 2g8r
17099236 S.Yajima, S.Inoue, T.Ogawa, T.Nonaka, K.Ohsawa, and H.Masaki (2006).
Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.
  Nucleic Acids Res, 34, 6074-6082.
PDB codes: 2dfx 2djh
16301790 D.E.Holloway, G.B.Chavali, M.C.Hares, V.Subramanian, and K.R.Acharya (2005).
Structure of murine angiogenin: features of the substrate- and cell-binding regions and prospects for inhibitor-binding studies.
  Acta Crystallogr D Biol Crystallogr, 61, 1568-1578.
PDB codes: 2bwk 2bwl
16045769 G.N.Hatzopoulos, D.D.Leonidas, R.Kardakaris, J.Kobe, and N.G.Oikonomakos (2005).
The binding of IMP to ribonuclease A.
  FEBS J, 272, 3988-4001.
PDB codes: 1z6d 1z6s
15273275 N.G.Beloglazova, M.M.Fabani, M.A.Zenkova, E.V.Bichenkova, N.N.Polushin, V.V.Sil'nikov, K.T.Douglas, and V.V.Vlassov (2004).
Sequence-specific artificial ribonucleases. I. Bis-imidazole-containing oligonucleotide conjugates prepared using precursor-based strategy.
  Nucleic Acids Res, 32, 3887-3897.  
14573867 D.D.Leonidas, G.B.Chavali, N.G.Oikonomakos, E.D.Chrysina, M.N.Kosmopoulou, M.Vlassi, C.Frankling, and K.R.Acharya (2003).
High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors.
  Protein Sci, 12, 2559-2574.
PDB codes: 1o0f 1o0h 1o0m 1o0n 1o0o
12356310 C.G.Mohan, E.Boix, H.R.Evans, Z.Nikolovski, M.V.Nogués, C.M.Cuchillo, and K.R.Acharya (2002).
The crystal structure of eosinophil cationic protein in complex with 2',5'-ADP at 2.0 A resolution reveals the details of the ribonucleolytic active site.
  Biochemistry, 41, 12100-12106.
PDB code: 1h1h
11742128 C.M.Cuchillo, M.Moussaoui, T.Barman, F.Travers, and M.V.Nogués (2002).
The exo- or endonucleolytic preference of bovine pancreatic ribonuclease A depends on its subsites structure and on the substrate size.
  Protein Sci, 11, 117-128.  
11876642 G.J.Swaminathan, D.E.Holloway, K.Veluraja, and K.R.Acharya (2002).
Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.
  Biochemistry, 41, 3341-3352.
PDB code: 1gqv
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
11264578 J.Pous, G.Mallorquí-Fernández, R.Peracaula, S.S.Terzyan, J.Futami, H.Tada, H.Yamada, M.Seno, R.de Llorens, F.X.Gomis-Rüth, and M.Coll (2001).
Three-dimensional structure of human RNase 1 delta N7 at 1.9 A resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 498-505.
PDB code: 1e21
11767103 M.Iwama, Y.Ogawa, K.Ohgi, T.Tsuji, and M.Irie (2001).
Enzymatic properties of sialic acid binding lectin from Rana catesbeiana modified with a water-soluble carbodiimide in the presence of various nucleophiles.
  Biol Pharm Bull, 24, 1366-1369.  
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.  
11087402 B.R.Kelemen, L.W.Schultz, R.Y.Sweeney, and R.T.Raines (2000).
Excavating an active site: the nucleobase specificity of ribonuclease A.
  Biochemistry, 39, 14487-14494.
PDB code: 1c8w
  10892814 L.Vitagliano, A.Merlino, A.Zagari, and L.Mazzarella (2000).
Productive and nonproductive binding to ribonuclease A: X-ray structure of two complexes with uridylyl(2',5')guanosine.
  Protein Sci, 9, 1217-1225.
PDB codes: 1eos 1eow
10547525 A.Peeters, and C.Van Alsenoy (1999).
Ab initio study of the reaction mechanism of ribonuclease A with cytidyl-3',5'-adenosine. I. Geometry optimization of cytidyl-3', 5'-adenosine.
  Biopolymers, 50, 697-704.  
10220316 B.R.Kelemen, and R.T.Raines (1999).
Extending the limits to enzymatic catalysis: diffusion of ribonuclease A in one dimension.
  Biochemistry, 38, 5302-5307.  
10049337 D.J.Quirk, and R.T.Raines (1999).
His ... Asp catalytic dyad of ribonuclease A: histidine pKa values in the wild-type, D121N, and D121A enzymes.
  Biophys J, 76, 1571-1579.  
10091597 E.H.Vatzaki, S.C.Allen, D.D.Leonidas, K.Trautwein-Fritz, J.Stackhouse, S.A.Benner, and K.R.Acharya (1999).
Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease--the basic surface, at 2.0 A resolution.
  Eur J Biochem, 260, 176-182.
PDB code: 1b6v
9724524 B.M.Fisher, J.H.Ha, and R.T.Raines (1998).
Coulombic forces in protein-RNA interactions: binding and cleavage by ribonuclease A and variants at Lys7, Arg10, and Lys66.
  Biochemistry, 37, 12121-12132.  
9521723 J.G.Opitz, M.I.Ciglic, M.Haugg, K.Trautwein-Fritz, S.A.Raillard, T.M.Jermann, S.A.Benner, and S.A.Benner (1998).
Origin of the catalytic activity of bovine seminal ribonuclease against double-stranded RNA.
  Biochemistry, 37, 4023-4033.  
  9514273 J.Hirschler, F.Halgand, E.Forest, and J.C.Fontecilla-Camps (1998).
Contaminant inclusion into protein crystals analyzed by electrospray mass spectrometry and X-ray crystallography.
  Protein Sci, 7, 185-192.  
  10082366 L.Vitagliano, S.Adinolfi, A.Riccio, F.Sica, A.Zagari, and L.Mazzarella (1998).
Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine.
  Protein Sci, 7, 1691-1699.
PDB code: 11ba
9154942 D.D.Leonidas, R.Shapiro, L.I.Irons, N.Russo, and K.R.Acharya (1997).
Crystal structures of ribonuclease A complexes with 5'-diphosphoadenosine 3'-phosphate and 5'-diphosphoadenosine 2'-phosphate at 1.7 A resolution.
  Biochemistry, 36, 5578-5588.
PDB codes: 1afk 1afl 1afu
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
  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.  
8570639 N.Russo, K.R.Acharya, B.L.Vallee, and R.Shapiro (1996).
A combined kinetic and modeling study of the catalytic center subsites of human angiogenin.
  Proc Natl Acad Sci U S A, 93, 804-808.  
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
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.