2RBI | pdb_00002rbi

STRUCTURE OF BINASE MUTANT HIS 101 ASN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 
    0.178 (Depositor), 0.158 (DCC) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

RNA cleavage without hydrolysis. Splitting the catalytic activities of binase with Asn101 and Thr101 mutations.

Okorokov, A.L.Panov, K.I.Offen, W.A.Mukhortov, V.G.Antson, A.A.Karpeisky, M.Y.a.Wilkinson, A.J.Dodson, G.G.

(1997) Protein Eng 10: 273-278

  • DOI: https://doi.org/10.1093/protein/10.3.273
  • Primary Citation Related Structures: 
    2RBI

  • PubMed Abstract: 

    Members of the microbial guanyl-specific ribonuclease family catalyse the endonucleolytic cleavage of single-stranded RNA in a two-step reaction involving transesterification to form a 2',3'-cyclic phosphate and its subsequent hydrolysis to yield the respective 3'-phosphate. The extracellular ribonuclease from Bacillus intermedius (binase, RNase Bi) shares a common mechanism for RNA hydrolysis with mammalian RNases. Two catalytic residues in the active site of binase, Glu72 and His101, are thought to be involved in general acid-general base catalysis of RNA cleavage. Using site-directed mutagenesis, binase mutants were produced containing amino acid substitutions H101N and H101T and their catalytic properties towards RNA, poly(I), poly(A), GpC and guanosine 2',3'-cyclic phosphate (cGMP) substrates were studied. The engineered mutant proteins are active in the transesterification step which produces the 2',3'-cyclic phosphate species but they have lost the ability to catalyse hydrolysis of the cyclic phosphate to give the 3' monophosphate product.


  • Organizational Affiliation
    • Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

Macromolecule Content 

  • Total Structure Weight: 24.41 kDa 
  • Atom Count: 1,947 
  • Modeled Residue Count: 216 
  • Deposited Residue Count: 218 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RIBONUCLEASE
A, B
109Bacillus intermediusMutation(s): 1 
Gene Names: PHOA-BINASE HIS101ASN
EC: 3.1.27
UniProt
Find proteins for P00649 (Bacillus intermedius)
Explore P00649 
Go to UniProtKB:  P00649
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00649
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work:  0.178 (Depositor), 0.158 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.26α = 90
b = 69.15β = 90
c = 33.37γ = 90
Software Package:
Software NamePurpose
CCP4model building
PROLSQrefinement
DENZOdata reduction
CCP4data scaling
ROTAVATAdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-03-12
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Other, Refinement description
  • Version 1.4: 2024-02-21
    Changes: Data collection
  • Version 1.5: 2024-04-03
    Changes: Refinement description