PDBsum entry 1x0f

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protein dna_rna links
Transcription/DNA PDB id
Protein chain
79 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription/DNA
Title: Complex structure of thE C-terminal RNA-binding domain of hnrnp d(auf1) with telomeric DNA
Structure: Heterogeneous nuclear ribonucleoprotein d0. Chain: a. Fragment: c-terminal RNA-binding domain. Synonym: hnrnp d0, au-rich element RNA-binding protein 1. Engineered: yes. 5'-d(p Tp Ap Gp G)-3'. Chain: b. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
NMR struc: 20 models
Authors: Y.Enokizono,Y.Konishi,K.Nagata,K.Ouhashi,S.Uesugi, F.Ishikawa,M.Katahira
Key ref:
Y.Enokizono et al. (2005). Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D. J Biol Chem, 280, 18862-18870. PubMed id: 15734733 DOI: 10.1074/jbc.M411822200
22-Mar-05     Release date:   05-Apr-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q14103  (HNRPD_HUMAN) -  Heterogeneous nuclear ribonucleoprotein D0
355 a.a.
79 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     2 terms  


DOI no: 10.1074/jbc.M411822200 J Biol Chem 280:18862-18870 (2005)
PubMed id: 15734733  
Structure of hnRNP D complexed with single-stranded telomere DNA and unfolding of the quadruplex by heterogeneous nuclear ribonucleoprotein D.
Y.Enokizono, Y.Konishi, K.Nagata, K.Ouhashi, S.Uesugi, F.Ishikawa, M.Katahira.
Heterogeneous nuclear ribonucleoprotein D, also known as AUF1, has two DNA/RNA-binding domains, each of which can specifically bind to single-stranded d(TTAGGG)n, the human telomeric repeat. Here, the structure of the C-terminal-binding domain (BD2) complexed with single-stranded d(TTAGGG) determined by NMR is presented. The structure has revealed that each residue of the d(TAG) segment is recognized by BD2 in a base-specific manner. The interactions deduced from the structure have been confirmed by gel retardation experiments with mutant BD2 and DNA. It is known that single-stranded DNA with the telomeric repeat tends to form a quadruplex and that the quadruplex has an inhibitory effect on telomere elongation by telomerase. This time it is revealed that BD2 unfolds the quadruplex of such DNA upon binding. Moreover, the effect of BD2 on the elongation by telomerase was examined in vitro. These results suggest the possible involvement of heterogeneous nuclear ribonucleoprotein D in maintenance of the telomere 3'-overhang either through protection of a single-stranded DNA or destabilization of the potentially deleterious quadruplex structure for the elongation by telomerase.
  Selected figure(s)  
Figure 3.
FIG. 3. Details of the recognition of Thy-2 (A), Ade-3 (B), and Gua-4 (C) of d(TTAGGG) by hnRNP D BD2. Hydrogen bonds are indicated by dotted lines.
Figure 4.
FIG. 4. Gel retardation experiments with mutant hnRNP D BD2s. A, Cy5-labeled d(GTCTTAGGGCGA) was incubated with either the wild type or mutant BD2 and then run on polyacrylamide gel. B, the intensity of the complex band relative to that for wild type BD2 is quantified for each mutant BD2. The results of three independent experiments were averaged.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 18862-18870) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20526337 C.Dominguez, J.F.Fisette, B.Chabot, and F.H.Allain (2010).
Structural basis of G-tract recognition and encaging by hnRNP F quasi-RRMs.
  Nat Struct Mol Biol, 17, 853-861.
PDB codes: 2kfy 2kg0 2kg1
  20563318 D.Yang, and K.Okamoto (2010).
Structural insights into G-quadruplexes: towards new anticancer drugs.
  Future Med Chem, 2, 619-646.  
20716519 T.M.Chen, C.H.Hsu, S.J.Tsai, and H.S.Sun (2010).
AUF1 p42 isoform selectively controls both steady-state and PGE2-induced FGF9 mRNA decay.
  Nucleic Acids Res, 38, 8061-8071.  
20670277 Y.Wu, and R.M.Brosh (2010).
G-quadruplex nucleic acids and human disease.
  FEBS J, 277, 3470-3488.  
19153609 A.Furukawa, T.Nagata, A.Matsugami, Y.Habu, R.Sugiyama, F.Hayashi, N.Kobayashi, S.Yokoyama, H.Takaku, and M.Katahira (2009).
Structure, interaction and real-time monitoring of the enzymatic reaction of wild-type APOBEC3G.
  EMBO J, 28, 440-451.
PDB code: 2kbo
18333962 A.B.Gyorgy, M.Szemes, Juan Romero, V.Tarabykin, and D.V.Agoston (2008).
SATB2 interacts with chromatin-remodeling molecules in differentiating cortical neurons.
  Eur J Neurosci, 27, 865-873.  
18515081 A.Cléry, M.Blatter, and F.H.Allain (2008).
RNA recognition motifs: boring? Not quite.
  Curr Opin Struct Biol, 18, 290-298.  
18158301 J.Tang, Z.Y.Kan, Y.Yao, Q.Wang, Y.H.Hao, and Z.Tan (2008).
G-quadruplex preferentially forms at the very 3' end of vertebrate telomeric DNA.
  Nucleic Acids Res, 36, 1200-1208.  
18953025 T.Nagata, Y.Takada, A.Ono, K.Nagata, Y.Konishi, T.Nukina, M.Ono, A.Matsugami, A.Furukawa, N.Fujimoto, H.Fukuda, H.Nakagama, and M.Katahira (2008).
Elucidation of the mode of interaction in the UP1-telomerase RNA-telomeric DNA ternary complex which serves to recruit telomerase to telomeric DNA and to enhance the telomerase activity.
  Nucleic Acids Res, 36, 6816-6824.  
17226803 L.Oganesian, and T.M.Bryan (2007).
Physiological relevance of telomeric G-quadruplex formation: a potential drug target.
  Bioessays, 29, 155-165.  
16885237 C.Dominguez, and F.H.Allain (2006).
NMR structure of the three quasi RNA recognition motifs (qRRMs) of human hnRNP F and interaction studies with Bcl-x G-tract RNA: a novel mode of RNA recognition.
  Nucleic Acids Res, 34, 3634-3645.
PDB codes: 2hgl 2hgm 2hgn
16943437 D.Churikov, C.Wei, and C.M.Price (2006).
Vertebrate POT1 restricts G-overhang length and prevents activation of a telomeric DNA damage checkpoint but is dispensable for overhang protection.
  Mol Cell Biol, 26, 6971-6982.  
17024178 I.Imbert, J.C.Guillemot, J.M.Bourhis, C.Bussetta, B.Coutard, M.P.Egloff, F.Ferron, A.E.Gorbalenya, and B.Canard (2006).
A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus.
  EMBO J, 25, 4933-4942.  
16914419 J.Eddy, and N.Maizels (2006).
Gene function correlates with potential for G4 DNA formation in the human genome.
  Nucleic Acids Res, 34, 3887-3896.  
17000771 L.Banihashemi, G.M.Wilson, N.Das, and G.Brewer (2006).
Upf1/Upf2 regulation of 3' untranslated region splice variants of AUF1 links nonsense-mediated and A+U-rich element-mediated mRNA decay.
  Mol Cell Biol, 26, 8743-8754.  
16511573 L.Oganesian, I.K.Moon, T.M.Bryan, and M.B.Jarstfer (2006).
Extension of G-quadruplex DNA by ciliate telomerase.
  EMBO J, 25, 1148-1159.  
17146462 N.Maizels (2006).
Dynamic roles for G4 DNA in the biology of eukaryotic cells.
  Nat Struct Mol Biol, 13, 1055-1059.  
16603717 Q.S.Zhang, L.Manche, R.M.Xu, and A.R.Krainer (2006).
hnRNP A1 associates with telomere ends and stimulates telomerase activity.
  RNA, 12, 1116-1128.  
16982642 S.D.Auweter, F.C.Oberstrass, and F.H.Allain (2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
  Nucleic Acids Res, 34, 4943-4959.  
16043710 A.J.Zaug, E.R.Podell, and T.R.Cech (2005).
Human POT1 disrupts telomeric G-quadruplexes allowing telomerase extension in vitro.
  Proc Natl Acad Sci U S A, 102, 10864-10869.  
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.