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PDBsum entry 1d9r
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dna_rna ligands links
DNA PDB id
1d9r

 

 

 

 

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Contents
DNA/RNA
Ligands
NCO
Waters ×133
PDB id:
1d9r
Name: DNA
Title: Crystal structure of DNA sheared tandem g-a base pairs
Structure: 5'-d( Cp Cp Gp Ap Ap (Bru)p Gp Ap Gp G)-3'. Chain: a, b. Engineered: yes
Source: Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.234     R-free:   0.278
Authors: Y.-G.Gao,H.Robinson,R.Sanishvili,A.Joachimiak,A.H.-J.Wang
Key ref:
Y.G.Gao et al. (1999). Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution. Biochemistry, 38, 16452-16460. PubMed id: 10600106 DOI: 10.1021/bi9914614
Date:
29-Oct-99     Release date:   05-Nov-99    
 Headers
 References

DNA/RNA chains
  C-C-G-A-A-BRU-G-A-G-G 10 bases
  C-C-G-A-A-BRU-G-A-G-G 10 bases

 

 
DOI no: 10.1021/bi9914614 Biochemistry 38:16452-16460 (1999)
PubMed id: 10600106  
 
 
Structure and recognition of sheared tandem G x A base pairs associated with human centromere DNA sequence at atomic resolution.
Y.G.Gao, H.Robinson, R.Sanishvili, A.Joachimiak, A.H.Wang.
 
  ABSTRACT  
 
G x A mismatched base pairs are frequently found in nucleic acids. Human centromere DNA sequences contain unusual repeating motifs, e.g. , (GAATG)n x (CATTC)n found in the human chromosome. The purine-rich strand of this repeating pentamer sequence forms duplex and hairpin structures with unusual stability. The high stability of these structures is contributed by the "sheared" G x A base pairs which present a novel recognition surface for ligands and proteins. We have solved the crystal structure, by the multiple-wavelength anomalous diffraction (MAD) method of d(CCGAATGAGG) in which the centromere core sequence motif GAATG is embedded. Three crystal forms were refined to near-atomic resolution. The structures reveal the detailed conformation of tandem G x A base pairs whose unique hydrogen-bonding surface has interesting interactions with bases, hydrated magnesium ions, cobalt(III)hexaammine, spermine, and water molecules. The results are relevant in understanding the structure associated with human centromere sequence in particular and G x A base pairs in nucleic acids (including RNA, like ribozyme) in general.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19244617 J.W.Locasale, A.A.Napoli, S.Chen, H.M.Berman, and C.L.Lawson (2009).
Signatures of protein-DNA recognition in free DNA binding sites.
  J Mol Biol, 386, 1054-1065.
PDB codes: 1hq7 2b1b 2b1c 2b1d
17882165 J.H.Min, and N.P.Pavletich (2007).
Recognition of DNA damage by the Rad4 nucleotide excision repair protein.
  Nature, 449, 570-575.
PDB codes: 2qsf 2qsg 2qsh
17367133 R.Carmieli, T.M.Larsen, G.H.Reed, S.Zein, F.Neese, and D.Goldfarb (2007).
The catalytic Mn2+ sites in the enolase-inhibitor complex: crystallography, single-crystal EPR, and DFT calculations.
  J Am Chem Soc, 129, 4240-4252.  
16461397 X.Liang, H.Kuhn, and M.D.Frank-Kamenetskii (2006).
Monitoring single-stranded DNA secondary structure formation by determining the topological state of DNA catenanes.
  Biophys J, 90, 2877-2889.  
15107489 M.H.Hou, H.Robinson, Y.G.Gao, and A.H.Wang (2004).
Crystal structure of the [Mg2+-(chromomycin A3)2]-d(TTGGCCAA)2 complex reveals GGCC binding specificity of the drug dimer chelated by a metal ion.
  Nucleic Acids Res, 32, 2214-2222.
PDB code: 1vaq
15048778 N.Korolev, A.P.Lyubartsev, A.Laaksonen, and L.Nordenskiöld (2004).
Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure.
  Biopolymers, 73, 542-555.  
15272160 T.P.Ko, H.M.Chu, C.Y.Chen, C.C.Chou, and A.H.Wang (2004).
Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.
  Acta Crystallogr D Biol Crystallogr, 60, 1381-1387.
PDB codes: 1wd0 1wd1
14993665 T.Sunami, J.Kondo, I.Hirao, K.Watanabe, K.Miura, and A.Takénaka (2004).
Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.
  Acta Crystallogr D Biol Crystallogr, 60, 422-431.
PDB codes: 1ub8 1ue4
12441336 B.L.Heidenfelder, A.M.Makhov, and M.D.Topal (2003).
Hairpin formation in Friedreich's ataxia triplet repeat expansion.
  J Biol Chem, 278, 2425-2431.  
12598364 J.A.Subirana, and M.Soler-Lopez (2003).
Cations as hydrogen bond donors: a view of electrostatic interactions in DNA.
  Annu Rev Biophys Biomol Struct, 32, 27-45.  
12777762 J.Deng, Y.Xiong, B.Pan, and M.Sundaralingam (2003).
Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 1004-1011.
PDB code: 1lnt
12433994 M.H.Hou, H.Robinson, Y.G.Gao, and A.H.Wang (2002).
Crystal structure of actinomycin D bound to the CTG triplet repeat sequences linked to neurological diseases.
  Nucleic Acids Res, 30, 4910-4917.
PDB code: 1mnv
11812845 M.H.Hou, S.B.Lin, J.M.Yuann, W.C.Lin, A.H.Wang, and L.Kan Ls (2001).
Effects of polyamines on the thermal stability and formation kinetics of DNA duplexes with abnormal structure.
  Nucleic Acids Res, 29, 5121-5128.  
11526315 M.L.Coté, and M.M.Georgiadis (2001).
Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs complexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase.
  Acta Crystallogr D Biol Crystallogr, 57, 1238-1250.
PDB code: 1i6j
11418770 S.Korolev, I.Dementieva, R.Sanishvili, W.Minor, Z.Otwinowski, and A.Joachimiak (2001).
Using surface-bound rubidium ions for protein phasing.
  Acta Crystallogr D Biol Crystallogr, 57, 1008-1012.  
10957631 M.L.Coté, S.J.Yohannan, and M.M.Georgiadis (2000).
Use of an N-terminal fragment from moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs.
  Acta Crystallogr D Biol Crystallogr, 56, 1120-1131.
PDB code: 1d1u
11087388 V.L.Murthy, and G.D.Rose (2000).
Is counterion delocalization responsible for collapse in RNA folding?
  Biochemistry, 39, 14365-14370.  
10998231 X.L.Yang, H.Robinson, Y.G.Gao, and A.H.Wang (2000).
Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms.
  Biochemistry, 39, 10950-10957.
PDB codes: 1fd5 1fdg
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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