1PGZ

Crystal Structure of UP1 Complexed With d(TTAGGGTTAG(6-MI)G); A Human Telomeric Repeat Containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6-MI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures

Myers, J.C.Moore, S.A.Shamoo, Y.

(2003) J.Biol.Chem. 278: 42300-42306

  • DOI: 10.1074/jbc.M306147200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heterogeneous ribonucleoprotein A1 (hnRNP A1) is an abundant nuclear protein that participates in RNA processing, alternative splicing, and chromosome maintenance. hnRNP A1 can be proteolyzed to unwinding protein (UP1), a 22.1-kDa protein that retain ...

    Heterogeneous ribonucleoprotein A1 (hnRNP A1) is an abundant nuclear protein that participates in RNA processing, alternative splicing, and chromosome maintenance. hnRNP A1 can be proteolyzed to unwinding protein (UP1), a 22.1-kDa protein that retains a high affinity for purine-rich single-stranded nucleic acids, including the human telomeric repeat (hTR) d(TTAGGG)n. Using the structure of UP1 bound to hTR as a guide, we have incorporated the fluorescent guanine analog 6-MI at one of two positions within the DNA to facilitate binding studies. One is where 6-MI remains stacked with an adjacent purine, and another is where it becomes fully unstacked upon UP1 binding. The structures of both modified oligonucleotides complexed to UP1 were determined by x-ray crystallography to validate the efficacy of our design, and 6-MI has proven to be an excellent reporter molecule for single-stranded nucleic acid interactions in positions where there is a change in stacking environment upon complex formation. We have shown that UP1 affinity for d(TTAGGG)2 is approximately 5 nm at 100 mm NaCl, pH 6.0, and our binding studies with d(TTAGG(6-MI)TTAGGG) show that binding is only modestly sensitive to salt and pH. UP1 also has a potent G-tetrad destabilizing activity that reduces the Tm of the hTR sequence d(TAGGGT)4 from 67.0 degrees C to 36.1 degrees C at physiological conditions (150 mm KCl, pH 7.0). Consistent with the structures determined by x-ray crystallography, UP1 is able to bind the hTR sequence in solution as a dimer and supports a model for hnRNP A1 binding to nucleic acids in arrays that may make a contiguous set of anti-parallel single-stranded nucleic acid binding clefts. These data suggest that seemingly disparate roles for hnRNP A1 in alternative splice site selection, RNA processing, RNA transport, and chromosome maintenance reflect its ability to bind a purine-rich consensus sequence (nYAGGn) and destabilize potentially deleterious G-tetrad structures.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, 6100 S. Main Street, Houston, TX 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heterogeneous nuclear ribonucleoprotein A1
A
195Homo sapiensMutation(s): 0 
Gene Names: HNRNPA1 (HNRPA1)
Find proteins for P09651 (Homo sapiens)
Go to Gene View: HNRNPA1
Go to UniProtKB:  P09651
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*T*TP*AP*GP*GP*GP*TP*TP*AP*GP*(6MI)P*G)-3'B12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MI
Query on 6MI
B
DNA LINKINGC12 H16 N5 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.622α = 90.00
b = 51.622β = 90.00
c = 171.472γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
Crystaldata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance