1B2M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis.

Arni, R.K.Watanabe, L.Ward, R.J.Kreitman, R.J.Kumar, K.Walz Jr., F.G.

(1999) Biochemistry 38: 2452-2461

  • DOI: 10.1021/bi982612q
  • Primary Citation of Related Structures:  
    1B2M

  • PubMed Abstract: 
  • The X-ray crystal structure of a complex between ribonuclease T1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2. 0 A resolution. This ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom ...

    The X-ray crystal structure of a complex between ribonuclease T1 and guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2. 0 A resolution. This ligand is an isosteric analogue of the minimal RNA substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted for the uridine 5'-oxygen atom. Two protein molecules are part of the asymmetric unit and both have a GpcU bound at the active site in the same manner. The protein-protein interface reveals an extended aromatic stack involving both guanines and three enzyme phenolic groups. A third GpcU has its guanine moiety stacked on His92 at the active site on enzyme molecule A and interacts with GpcU on molecule B in a neighboring unit via hydrogen bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine moieties of the three GpcU molecules in the asymmetric unit interacts directly with the protein. GpcU-active-site interactions involve extensive hydrogen bonding of the guanine moiety at the primary recognition site and of the guanosine 2'-hydroxyl group with His40 and Glu58. On the other hand, the phosphonate group is weakly bound only by a single hydrogen bond with Tyr38, unlike ligand phosphate groups of other substrate analogues and 3'-GMP, which hydrogen-bonded with three additional active-site residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate moiety is essentially the same as that recently observed for a novel structure of a RNase T1-3'-GMP complex obtained immediately after in situ hydrolysis of exo-(Sp)-guanosine 2',3'-cyclophosphorothioate [Zegers et al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the active site represents a nonproductive binding mode for GpU [Steyaert, J., and Engleborghs (1995) Eur. J. Biochem. 233, 140-144]. The results suggest that the active site of ribonuclease T1 is adapted for optimal tight binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in the transition state for catalytic transesterification, which is stabilized by adjacent binding of the leaving nucleoside (U) group.


    Related Citations: 
    • Three-Dimensional Structure of Gln 25-Ribonuclease T1 at 1.84 Angstroms Resolution: Structural Variations at the Base Recognition and Catalytic Sites
      Arni, R.K., Pal, G.P., Ravichandran, K.G., Tulinsky, A., Metcalf Jr., P.F.G.W.
      (1992) Biochemistry 31: 3126
    • Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding
      Kostrewa, D., Choe, H.-W., Heinemann, U., Saenger, W.
      (1989) Biochemistry 28: 7592
    • Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution
      Arni, R., Heinemann, U., Tokuoka, R., Saenger, W.
      (1988) J Biol Chem 263: 15358
    • Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
      Arni, R., Heinemann, V., Maslowska, M., Tokuoka, R., Saenger, W.
      (1987) Acta Crystallogr B 43: 548
    • Structure and Function of the Enzyme Ribonuclease T1
      Arni, R., Heinemann, U., Saenger, W.
      (1987) Fresenius Z für Anal Chem 327: 67
    • Crystallization of Ribonuclease T1
      Martin, P.O., Tulinsky, A., Walz, F.G.
      (1980) J Mol Biol 136: 95

    Organizational Affiliation

    Department of Physics, UNESP/IBILCE, S. J. do Rio Preto-SP, Brazil.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE T1D [auth A], E [auth B]104Aspergillus oryzaeMutation(s): 0 
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
Find proteins for P00651 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P00651 
Go to UniProtKB:  P00651
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*GP*(U34))-3'A [auth C], B [auth D], C [auth E]2N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.254 
    • R-Value Work: 0.187 
    • R-Value Observed: 0.187 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 69.91α = 90
    b = 90.29β = 90
    c = 33.98γ = 90
    Software Package:
    Software NamePurpose
    AMoREphasing
    X-PLORrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1999-03-25
      Type: Initial release
    • Version 1.1: 2008-04-26
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2017-02-01
      Changes: Structure summary