› 1b2m

X-ray diffraction
2Å resolution

THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.

Released:
DOI: 10.2210/pdb1b2m/pdb
PDB entry 1b2m coloured by chain, front view.
PDB entry 1b2m coloured by chain, side view.
PDB entry 1b2m coloured by chain, top view.
Source organism: Aspergillus oryzae
Primary publication:
Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis.
Arni RK, Watanabe L, Ward RJ, Kreitman RJ, Kumar K, Walz FG
Biochemistry 38 2452-61 (1999)
PMID: 10029539

Function and Biology Details

Reaction catalysed: 
(1a) (RNA) containing guanosine = (RNA fragment)-3'-guanosine-2',3'-cyclophosphate + a 5'-hydroxy-ribonucleotide-3'-(RNA fragment)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero trimer
Assembly name:
PDBe Complex ID:
PDB-CPX-132809 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Guanyl-specific ribonuclease T1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 104 amino acids
Theoretical weight: 11.09 KDa
Source organism: Aspergillus oryzae
UniProt:
  • Canonical: P00651 (Residues: 27-130; Coverage: 100%)
Gene names: AO090011000118, rntA
Structure domains: Microbial ribonucleases
5'-R(*GP*(U34))-3' Chains: C, D, E
Molecule details ›
Chains: C, D, E
Length: 2 nucleotides
Theoretical weight: 620 Da
Source organism: Aspergillus oryzae
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand U34 3 x U34

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 69.91Å b: 90.29Å c: 33.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.187 0.254
Expression system: Not provided

Quick links

Citations

1 review citation

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
7 other articles

4 mentions without citation

Not making the cut: Techniques to prevent RNA cleavage in structural studies of RNase-RNA complexes.
Jones et al. (2022)
3 more