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PDBsum entry 1gsp
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protein ligands metals links
Endoribonuclease PDB id
1gsp

 

 

 

 

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Contents
Protein chain
104 a.a. *
Ligands
SGP
Metals
_CA
Waters ×123
* Residue conservation analysis
PDB id:
1gsp
Name: Endoribonuclease
Title: Ribonuclease t1 complexed with 2',3'-cgps, 1 day
Structure: Ribonuclease t1. Chain: a. Synonym: rnase t1. Engineered: yes. Other_details: complex with guanosine 2',3' cyclic phosphorothioate
Source: Aspergillus oryzae. Organism_taxid: 5062. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.20Å     R-factor:   0.151     R-free:   0.206
Authors: I.Zegers,L.Wyns
Key ref: I.Zegers et al. (1998). Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography. Nat Struct Biol, 5, 280-283. PubMed id: 9546218
Date:
28-Nov-97     Release date:   25-Feb-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00651  (RNT1_ASPOR) -  Guanyl-specific ribonuclease T1 from Aspergillus oryzae (strain ATCC 42149 / RIB 40)
Seq:
Struc: 		130 a.a.
104 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.4.6.1.24  - ribonuclease T1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]

 

 
Nat Struct Biol 5:280-283 (1998)
PubMed id: 9546218  
 
 
Hydrolysis of a slow cyclic thiophosphate substrate of RNase T1 analyzed by time-resolved crystallography.
I.Zegers, R.Loris, G.Dehollander, A.Fattah Haikal, F.Poortmans, J.Steyaert, L.Wyns.
 
  ABSTRACT  
 
Here we present a time-resolved crystallographic analysis of the hydrolysis of exo (Sp) guanosine 2',3'-cyclophosphorothioate by RNase T1. The use of a slow substrate and fast crystallization methods made it possible to perform the study with conventional data-collection techniques. The results support the idea that the hydrolysis reaction proceeds through a mechanism that is the inverse of the transesterification reaction. In addition, the structures provide an explanation for the differential behavior of RNase T1 towards exo- and endo-cyclic thiophosphates.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20855293 B.Meineke, B.Schwer, R.Schaffrath, and S.Shuman (2011).
Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC.
  Nucleic Acids Res, 39, 687-700.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
19383764 N.Keppetipola, R.Jain, B.Meineke, M.Diver, and S.Shuman (2009).
Structure-activity relationships in Kluyveromyces lactis gamma-toxin, a eukaryal tRNA anticodon nuclease.
  RNA, 15, 1036-1044.  
19558492 V.Bauerová-Hlinková, R.Dvorský, D.Perecko, F.Povazanec, and J.Sevcík (2009).
Structure of RNase Sa2 complexes with mononucleotides--new aspects of catalytic reaction and substrate recognition.
  FEBS J, 276, 4156-4168.
PDB codes: 3d4a 3d5g 3d5i 3dgy 3dh2
18757371 N.Keppetipola, and S.Shuman (2008).
A Phosphate-binding Histidine of Binuclear Metallophosphodiesterase Enzymes Is a Determinant of 2',3'-Cyclic Nucleotide Phosphodiesterase Activity.
  J Biol Chem, 283, 30942-30949.  
18305191 S.M.Rodriguez, S.Panjikar, K.Van Belle, L.Wyns, J.Messens, and R.Loris (2008).
Nonspecific base recognition mediated by water bridges and hydrophobic stacking in ribonuclease I from Escherichia coli.
  Protein Sci, 17, 681-690.
PDB code: 2z70
16740124 E.Alvarez-García, L.García-Ortega, Y.Verdún, M.Bruix, A.Martínez del Pozo, and J.G.Gavilanes (2006).
Tyr-48, a conserved residue in ribotoxins, is involved in the RNA-degrading activity of alpha-sarcin.
  Biol Chem, 387, 535-541.  
12122018 P.Mignon, J.Steyaert, R.Loris, P.Geerlings, and S.Loverix (2002).
A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study.
  J Biol Chem, 277, 36770-36774.
PDB codes: 1lov 1low 1loy
11331007 A.V.Kravchuk, L.Zhao, R.J.Kubiak, K.S.Bruzik, and M.D.Tsai (2001).
Mechanism of phosphatidylinositol-specific phospholipase C: origin of unusually high nonbridging thio effects.
  Biochemistry, 40, 5433-5439.  
11453993 J.Deswarte, S.De Vos, U.Langhorst, J.Steyaert, and R.Loris (2001).
The contribution of metal ions to the conformational stability of ribonuclease T1: crystal versus solution.
  Eur J Biochem, 268, 3993-4000.
PDB codes: 1hyf 1hz1 1i0v 1i0x
11733014 M.Masip, J.Lacadena, J.M.Mancheño, M.Oñaderra, A.Martínez-Ruiz, A.Martínez del Pozo, and J.G.Gavilanes (2001).
Arginine 121 is a crucial residue for the specific cytotoxic activity of the ribotoxin alpha-sarcin.
  Eur J Biochem, 268, 6190-6196.  
11114513 I.Schlichting, and K.Chu (2000).
Trapping intermediates in the crystal: ligand binding to myoglobin.
  Curr Opin Struct Biol, 10, 744-752.  
11048955 S.Loverix, A.Winqvist, R.Strömberg, and J.Steyaert (2000).
Mechanism of RNase T1: concerted triester-like phosphoryl transfer via a catalytic three-centered hydrogen bond.
  Chem Biol, 7, 651-658.  
9927651 I.Zegers, J.Deswarte, and L.Wyns (1999).
Trimeric domain-swapped barnase.
  Proc Natl Acad Sci U S A, 96, 818-822.
PDB code: 1yvs
10373011 R.Loris, U.Langhorst, S.De Vos, K.Decanniere, J.Bouckaert, D.Maes, T.R.Transue, and J.Steyaert (1999).
Conserved water molecules in a large family of microbial ribonucleases.
  Proteins, 36, 117-134.
PDB codes: 1bu4 2bu4 3bu4 4bu4 5bu4
9586998 S.Loverix, A.Winquist, R.Strömberg, and J.Steyaert (1998).
An engineered ribonuclease preferring phosphorothioate RNA.
  Nat Struct Biol, 5, 365-368.  
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.

 

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