3HF1

Crystal structure of human p53R2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

2.6 A X-ray crystal structure of human p53R2, a p53-inducible ribonucleotide reductase .

Smith, P.Zhou, B.Ho, N.Yuan, Y.C.Su, L.Tsai, S.C.Yen, Y.

(2009) Biochemistry 48: 11134-11141

  • DOI: 10.1021/bi9001425

  • PubMed Abstract: 
  • Human p53R2 (hp53R2) is a 351-residue p53-inducible ribonucleotide reductase (RNR) small subunit. It shares >80% sequence identity with hRRM2, the small RNR subunit responsible for normal maintenance of the deoxyribonucleotide (dNTP) pool used for DN ...

    Human p53R2 (hp53R2) is a 351-residue p53-inducible ribonucleotide reductase (RNR) small subunit. It shares >80% sequence identity with hRRM2, the small RNR subunit responsible for normal maintenance of the deoxyribonucleotide (dNTP) pool used for DNA replication, which is active during the S phase in a cell cycle-dependent fashion. But rather than cyclic dNTP synthesis, hp53R2 has been shown to supply dNTPs for DNA repair to cells in G0-G1 in a p53-dependent fashion. The first X-ray crystal structure of hp53R2 is determined to 2.6 A, in which monomers A and B exhibit mono- and binuclear iron occupancy, respectively. The pronounced structural differences at three regions between hp53R2 and hRRM2 highlight the possible regulatory role in iron assimilation and help explain previously observed physical and biochemical differences in the mobility and accessibility of the radical iron center, as well as radical transfer pathways between the two enzymes. The sequence-structure-function correlations that differentiate hp53R2 and hRRM2 are revealed for the first time. Insight gained from this structural work will be used in the identification of biological function, regulation mechanism, and inhibitor selection in RNR small subunits.


    Organizational Affiliation

    Department of Chemistry, University of California, Irvine, California 92697, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonucleoside-diphosphate reductase subunit M2 B
A, B
351Homo sapiensMutation(s): 0 
Gene Names: RRM2B (P53R2)
EC: 1.17.4.1
Find proteins for Q7LG56 (Homo sapiens)
Go to Gene View: RRM2B
Go to UniProtKB:  Q7LG56
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.675α = 90.00
b = 99.546β = 90.00
c = 132.190γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-19
    Type: Database references