PDBsum entry 1rtu

Go to PDB code: 
protein ligands links
Hydrolase PDB id
Protein chain
114 a.a. *
Waters ×141
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Ustilago sphaerogena ribonuclease u2
Structure: Ribonuclease u2. Chain: a
Source: Ustilago sphaerogena. Organism_taxid: 5271. Atcc: 12421
1.80Å     R-factor:   0.143     R-free:   0.178
Authors: S.Noguchi,Y.Satow,T.Uchida,C.Sasaki,T.Matsuzaki
Key ref:
S.Noguchi et al. (1995). Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution. Biochemistry, 34, 15583-15591. PubMed id: 7492561 DOI: 10.1021/bi00047a025
12-May-95     Release date:   08-Nov-96    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00654  (RNU2_USTSP) -  Ribonuclease U2
114 a.a.
114 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Ribonuclease U(2).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in A-P or G-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   4 terms 
  Biochemical function     hydrolase activity     8 terms  


DOI no: 10.1021/bi00047a025 Biochemistry 34:15583-15591 (1995)
PubMed id: 7492561  
Crystal structure of Ustilago sphaerogena ribonuclease U2 at 1.8 A resolution.
S.Noguchi, Y.Satow, T.Uchida, C.Sasaki, T.Matsuzaki.
The crystal structure of purine-specific ribonuclease (RNase) U2 from Ustilago sphaerogena has been solved by the molecular replacement methods using RNase T1 as a search model. The structure, with 114 amino acid residues, 141 water molecules, and a sulfate ion, is refined to an R factor of 0.143 at 1.8 A resolution. As evidenced by the electron densities, residues 49 and 50 are revised to Glu 49 and Asp 50, respectively, and also Asp 45 is identified as a beta-isomerized form to L-isoaspartate with a beta-peptide linkage. RNase U2 consists of a beta-hairpin at residues from 7 to 14, a 4.4-turn alpha-helix from 16 to 32, a central beta-sheet with five strands, and a protruding beta-turn from 74 to 77. As for the catalytic site residues, His 41, Glu 62, and Arg 85 are located as constituents of the central beta-sheet, and Tyr 39 and His 101 are situated at either end of the beta-sheet. The side chains of Tyr 39, Glu 62, Arg 85, and His 101 are hydrogen-bonded to the sulfate ion which marks the RNA phosphate position. Though the side chain of His 41 is pointing away from the sulfate, small conformational adjustments of His 41 enable the side chain to interact with either the phosphate or the ribose group of RNA. The loop region from Tyr 44 to Asp 50 is ascribed to the base recognition site where Glu 49 is involved in adenine recognition. beta-Isomerized Asp 45 suggests that this region is conformationally flexible and alterable.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20606265 S.Noguchi (2010).
Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate.
  Acta Crystallogr D Biol Crystallogr, 66, 843-849.
PDB codes: 3agn 3ago
20623666 S.Noguchi (2010).
Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B.
  Biopolymers, 93, 1003-1010.
PDB code: 3ahs
17253975 J.Lacadena, E.Alvarez-García, N.Carreras-Sangrà, E.Herrero-Galán, J.Alegre-Cebollada, L.García-Ortega, M.Oñaderra, J.G.Gavilanes, and A.Martínez del Pozo (2007).
Fungal ribotoxins: molecular dissection of a family of natural killers.
  FEMS Microbiol Rev, 31, 212-237.  
16110465 L.García-Ortega, V.De los Ríos, A.Martínez-Ruiz, M.Oñaderra, J.Lacadena, A.Martínez del Pozo, and J.G.Gavilanes (2005).
Anomalous electrophoretic behavior of a very acidic protein: ribonuclease U2.
  Electrophoresis, 26, 3407-3413.  
11847284 C.D.Smith, M.Carson, A.M.Friedman, M.M.Skinner, L.Delucas, L.Chantalat, L.Weise, T.Shirasawa, and D.Chattopadhyay (2002).
Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.
  Protein Sci, 11, 625-635.
PDB code: 1i1n
11897788 L.Garcia-Ortega, M.Masip, J.M.Mancheño, M.Oñaderra, M.A.Lizarbe, M.F.García-Mayoral, M.Bruix, A.Martínez del Pozo, and J.G.Gavilanes (2002).
Deletion of the NH2-terminal beta-hairpin of the ribotoxin alpha-sarcin produces a nontoxic but active ribonuclease.
  J Biol Chem, 277, 18632-18639.  
11297444 K.Kumar, and F.G.Walz (2001).
Probing functional perfection in substructures of ribonuclease T1: double combinatorial random mutagenesis involving Asn43, Asn44, and Glu46 in the guanine binding loop.
  Biochemistry, 40, 3748-3757.  
11468362 L.García-Ortega, J.Lacadena, J.M.Mancheño, M.Oñaderra, R.Kao, J.Davies, N.Olmo, Pozo AM, and J.G.Gavilanes (2001).
Involvement of the amino-terminal beta-hairpin of the Aspergillus ribotoxins on the interaction with membranes and nonspecific ribonuclease activity.
  Protein Sci, 10, 1658-1668.  
11296285 N.E.Robinson, and A.B.Robinson (2001).
Prediction of protein deamidation rates from primary and three-dimensional structure.
  Proc Natl Acad Sci U S A, 98, 4367-4372.  
  10930732 A.Martínez-Ruiz, L.García-Ortega, R.Kao, M.Oñaderra, J.M.Mancheño, J.Davies, A.Martínez del Pozo, and J.G.Gavilanes (2000).
Ribonuclease U2: cloning, production in Pichia pastoris and affinity chromatography purification of the active recombinant protein.
  FEMS Microbiol Lett, 189, 165-169.  
11080641 M.M.Skinner, J.M.Puvathingal, R.L.Walter, and A.M.Friedman (2000).
Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair.
  Structure, 8, 1189-1201.
PDB code: 1dl5
10842342 S.Eschenburg, and E.Schönbrunn (2000).
Comparative X-ray analysis of the un-liganded fosfomycin-target murA.
  Proteins, 40, 290-298.
PDB codes: 1ejc 1ejd
10961544 T.Meguro, T.Kashiwagi, and Y.Satow (2000).
Crystal structure of the low-humidity form of aspartame sweetener.
  J Pept Res, 56, 97.  
10771427 U.Rester, M.Moser, R.Huber, and W.Bode (2000).
L-Isoaspartate 115 of porcine beta-trypsin promotes crystallization of its complex with bdellastasin.
  Acta Crystallogr D Biol Crystallogr, 56, 581-588.
PDB code: 1eja
10591106 J.Lacadena, A.Martínez del Pozo, A.Martínez-Ruiz, J.M.Pérez-Cañadillas, M.Bruix, J.M.Mancheño, M.Oñaderra, and J.G.Gavilanes (1999).
Role of histidine-50, glutamic acid-96, and histidine-137 in the ribonucleolytic mechanism of the ribotoxin alpha-sarcin.
  Proteins, 37, 474-484.  
9354640 S.K.Nayak, and J.K.Batra (1997).
A single amino acid substitution in ribonucleolytic toxin restrictocin abolishes its specific substrate recognition activity.
  Biochemistry, 36, 13693-13699.  
8805570 X.Yang, and K.Moffat (1996).
Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin.
  Structure, 4, 837-852.
PDB code: 1aqz
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.