1UN3

CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN VARIANT T44D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic Studies on Structural Features that Determine the Enzymatic Specificity and Potency of Human Angiogenin: Thr44, Thr80 and Residues 38-41

Holloway, D.E.Chavali, G.B.Hares, M.C.Baker, M.D.Subbarao, G.V.Shapiro, R.Acharya, K.R.

(2004) Biochemistry 43: 1230

  • DOI: 10.1021/bi035654+
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human angiogenin (Ang) is a potent inducer of blood vessel formation and is a member of the pancreatic ribonuclease superfamily. Its enzymatic activity is unusually weak and biased toward cleavage after cytidine nucleotides. As part of an ongoing inv ...

    Human angiogenin (Ang) is a potent inducer of blood vessel formation and is a member of the pancreatic ribonuclease superfamily. Its enzymatic activity is unusually weak and biased toward cleavage after cytidine nucleotides. As part of an ongoing investigation into the structural basis of Ang's characteristic activity, we have determined the crystal structures of three Ang variants having novel activity. (i) The structure of T44D-Ang indicates that Asp44 can participate directly in pyrimidine binding and that the intrinsic hydrogen-bonding capability of this residue largely governs the pyrimidine specificity of this variant. Unexpectedly, the mutation also causes the most extensive disruption of the C-terminus seen in any Ang variant thus far. This allows the side chain of Arg101 to penetrate the B(1) site, raising the possibility that it participates in substrate binding as occurs in ribonuclease 4. (ii) The structure of T80A-Ang supports the view that Thr80 plays little role in maintaining the obstructive conformation of the C-terminus and that its participation in a hydrogen bond with Thr44 selectively weakens the interaction between Thr44 and N3 of cytosine. (iii) ARH-II is an angiogenin/RNase A chimera in which residues 38-41 of Ang are replaced with the corresponding residues (38-42) of RNase A. Its structure suggests that the guest segment influences catalysis by subtle means, possibly by reducing the pK(a) of the catalytic lysine. The loss of angiogenic activity is not attributable to disruption of known cell-binding or nuclear translocation sites but may be a consequence of the chimera's enhanced ribonucleolytic activity.


    Related Citations: 
    • Alteration of the Enzymatic Specificity of Human Angiogenin by Site-Directed Mutagenesis
      Curran, T.P.,Shapiro, R.,Riordan, J.F.
      (1993) Biochemistry 32: 2307
    • Refined Crystal Structures of Native Human Angiogenin and Two Active Site Variants: Implications for the Unique Functional Properties of an Enzyme Involved in Neovascularisation During Tumour Growth
      Leonidas, D.D.,Shapiro, R.,Allen, S.C.,Subbarao, G.V.,Veluraja, K.,Acharya, K.R.
      (1999) J.Mol.Biol. 285: 1209


    Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ANGIOGENIN
A
123Homo sapiensMutation(s): 1 
Gene Names: ANG (RNASE5)
EC: 3.1.27.-
Find proteins for P03950 (Homo sapiens)
Go to Gene View: ANG
Go to UniProtKB:  P03950
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.398α = 90.00
b = 41.533β = 90.00
c = 33.761γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance