2LRR

Solution structure of the R3H domain from human Smubp-2 in complex with 2'-deoxyguanosine-5'-monophosphate


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Basis for 5'-End-Specific Recognition of Single-Stranded DNA by the R3H Domain from Human Smubp-2

Jaudzems, K.Jia, X.Yagi, H.Zhulenkovs, D.Graham, B.Otting, G.Liepinsh, E.

(2012) J.Mol.Biol. 12: 760-767

  • DOI: 10.1016/j.jmb.2012.09.010

  • PubMed Abstract: 
  • The R3H domain is a conserved sequence motif in nucleic acid binding proteins. Previously, we reported the solution structure of the R3H domain and identified a putative nucleic acid binding site composed of three conserved basic residues [Liepinsh, ...

    The R3H domain is a conserved sequence motif in nucleic acid binding proteins. Previously, we reported the solution structure of the R3H domain and identified a putative nucleic acid binding site composed of three conserved basic residues [Liepinsh, E., Leonchiks, A., Sharipo, A., Guignard, L. & Otting, G. (2003). Solution structure of the R3H domain from human Sμbp-2. J. Mol. Biol.326, 217-223]. Here, we determine the binding affinities of mononucleotides and dinucleotides for the R3H domain from human Sμbp-2 (Sμbp2-R3H) and map their binding sites on the protein's surface. Although the binding affinities show up to 260-fold selectivity between different nucleotides, their binding sites and conformations seem very similar. Further, we report the NMR structure of the Sμbp2-R3H in complex with deoxyguanosine 5'-monophosphate (dGMP) mimicking the 5'-end of single-stranded DNA. Pseudocontact shifts from a paramagnetic lanthanide tag attached to residue 731 in the mutant A731C confirmed that binding of dGMP brings a loop of the protein into closer proximity. The structure provides the first structural insight into single-stranded nucleic acid recognition by the R3H domain and shows that the R3H domain specifically binds the phosphorylated 5'-end through electrostatic interactions with the two conserved arginines and stacking interactions with the highly conserved histidine.


    Organizational Affiliation

    Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Latvia. kristaps.jaudzems@osi.lv




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein SMUBP-2
A
86Homo sapiensMutation(s): 0 
Gene Names: IGHMBP2 (SMBP2, SMUBP2)
EC: 3.6.4.12, 3.6.4.13
Find proteins for P38935 (Homo sapiens)
Go to Gene View: IGHMBP2
Go to UniProtKB:  P38935
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGP
Query on DGP

Download SDF File 
Download CCD File 
A
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 
  • Olderado: 2LRR Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release