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PDBsum entry 1zzi

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protein dna_rna Protein-protein interface(s) links
Structural protein/DNA PDB id
1zzi
Jmol
Contents
Protein chains
82 a.a. *
DNA/RNA
Waters ×136
* Residue conservation analysis
PDB id:
1zzi
Name: Structural protein/DNA
Title: Crystal structure analysis of the third kh domain of hnrnp k complex with ssdna
Structure: 5'-d( Cp Tp Cp Cp Cp C)-3'. Chain: c, d. Engineered: yes. Heterogeneous nuclear ribonucleoprotein k. Chain: a, b. Fragment: kh3 domain. Synonym: hnrnp k, transformation up-regulated nuclear prote engineered: yes
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.197     R-free:   0.240
Authors: P.H.Backe,A.C.Messias,R.B.Ravelli,M.Sattler,S.Cusack
Key ref:
P.H.Backe et al. (2005). X-ray crystallographic and NMR studies of the third KH domain of hnRNP K in complex with single-stranded nucleic acids. Structure, 13, 1055-1067. PubMed id: 16004877 DOI: 10.1016/j.str.2005.04.008
Date:
14-Jun-05     Release date:   09-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61978  (HNRPK_HUMAN) -  Heterogeneous nuclear ribonucleoprotein K
Seq:
Struc:
463 a.a.
82 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     RNA binding     1 term  

 

 
DOI no: 10.1016/j.str.2005.04.008 Structure 13:1055-1067 (2005)
PubMed id: 16004877  
 
 
X-ray crystallographic and NMR studies of the third KH domain of hnRNP K in complex with single-stranded nucleic acids.
P.H.Backe, A.C.Messias, R.B.Ravelli, M.Sattler, S.Cusack.
 
  ABSTRACT  
 
The heterogeneous nuclear ribonucleoprotein (hnRNP) K is implicated in multiple functions in the regulation of gene expression and acts as a hub at the intersection of signaling pathways and processes involving nucleic acids. Central to its function is its ability to bind both ssDNA and ssRNA via its KH (hnRNP K homology) domains. We determined crystal structures of hnRNP K KH3 domain complexed with 15-mer and 6-mer (CTC(4)) ssDNAs at 2.4 and 1.8 A resolution, respectively, and show that the KH3 domain binds specifically to both TCCC and CCCC sequences. In parallel, we used NMR to compare the binding affinity and mode of interaction of the KH3 domain with several ssRNA ligands and CTC(4) ssDNA. Based on a structure alignment of the KH3-CTC(4) complex with known structures of other KH domains in complex with ssRNA, we discuss recognition of tetranucleotide sequences by KH domains.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Detailed View of the KH3-CTC[4] Complex
(A) Stereo diagram showing conserved conformation of the central tetranucleotide in the two examples of the KH3-CTC[4] complex.
(B) Stereo view showing how Gly400 and Ile403 are inserted like a wedge, preventing the base stacking of Thy2, Cyt3, and Cyt4.
(C) sA-weighted 2F[o] - F[c] electron density contoured at 1.0 s (blue) showing the recognition of the first nucleotide, thymine, in the core recognition sequence.
(D) sA-weighted 2F[o] - F[c] electron density contoured at 1.0 s (blue) of the interactions of the two middle nucleotides (Cyt3 and Cyt4) in the core recognition sequence with the protein.
(E) Stereo view showing the water-mediated hydrogen bonds and base stacking of Cyt5. Water molecules are indicated as red spheres, and hydrogen bonds are indicated as green dashed lines.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1055-1067) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23142982 G.Nicastro, M.F.García-Mayoral, D.Hollingworth, G.Kelly, S.R.Martin, P.Briata, R.Gherzi, and A.Ramos (2012).
Noncanonical G recognition mediates KSRP regulation of let-7 biogenesis.
  Nat Struct Mol Biol, 19, 1282-1286.
PDB code: 4b8t
  21410645 M.Doetsch, R.Schroeder, and B.Fürtig (2011).
Transient RNA-protein interactions in RNA folding.
  FEBS J, 278, 1634-1642.  
20080952 J.A.Chao, Y.Patskovsky, V.Patel, M.Levy, S.C.Almo, and R.H.Singer (2010).
ZBP1 recognition of beta-actin zipcode induces RNA looping.
  Genes Dev, 24, 148-158.
PDB code: 3krm
20795951 S.P.Han, Y.H.Tang, and R.Smith (2010).
Functional diversity of the hnRNPs: past, present and perspectives.
  Biochem J, 430, 379-392.  
19457263 A.Galarneau, and S.Richard (2009).
The STAR RNA binding proteins GLD-1, QKI, SAM68 and SLM-2 bind bipartite RNA motifs.
  BMC Mol Biol, 10, 47.  
19641227 J.Grillari, M.Löscher, M.Denegri, K.Lee, K.Fortschegger, F.Eisenhaber, P.Ajuh, A.I.Lamond, H.Katinger, and R.Grillari-Voglauer (2009).
Blom7alpha is a novel heterogeneous nuclear ribonucleoprotein K homology domain protein involved in pre-mRNA splicing that interacts with SNEVPrp19-Pso4.
  J Biol Chem, 284, 29193-29204.  
18441016 I.S.Naarmann, C.Harnisch, N.Flach, E.Kremmer, H.Kühn, D.H.Ostareck, and A.Ostareck-Lederer (2008).
mRNA silencing in human erythroid cell maturation: heterogeneous nuclear ribonucleoprotein K controls the expression of its regulator c-Src.
  J Biol Chem, 283, 18461-18472.  
18701464 Z.Du, S.Fenn, R.Tjhen, and T.L.James (2008).
Structure of a Construct of a Human Poly(C)-binding Protein Containing the First and Second KH Domains Reveals Insights into Its Regulatory Mechanisms.
  J Biol Chem, 283, 28757-28766.  
17612614 A.M.Leopoldino, F.Carregaro, C.H.Silva, O.Feitosa, U.M.Mancini, J.M.Freitas, and E.H.Tajara (2007).
Sequence and transcriptional study of HNRPK pseudogenes, and expression and molecular modeling analysis of hnRNP K isoforms.
  Genome, 50, 451-462.  
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
17267406 K.Buchet-Poyau, J.Courchet, H.Le Hir, B.Séraphin, J.Y.Scoazec, L.Duret, C.Domon-Dell, J.N.Freund, and M.Billaud (2007).
Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies.
  Nucleic Acids Res, 35, 1289-1300.  
17264125 M.A.Brykailo, A.H.Corbett, and J.L.Fridovich-Keil (2007).
Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160.
  Nucleic Acids Res, 35, 1108-1118.  
17426136 S.Fenn, Z.Du, J.K.Lee, R.Tjhen, R.M.Stroud, and T.L.James (2007).
Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution.
  Nucleic Acids Res, 35, 2651-2660.
PDB code: 2p2r
17526645 Z.Du, J.K.Lee, S.Fenn, R.Tjhen, R.M.Stroud, and T.L.James (2007).
X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2.
  RNA, 13, 1043-1051.
PDB codes: 2pqu 2py9
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.  
16186123 Z.Du, J.K.Lee, R.Tjhen, S.Li, H.Pan, R.M.Stroud, and T.L.James (2005).
Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A.
  J Biol Chem, 280, 38823-38830.
PDB code: 2axy
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 code is shown on the right.