PDBsum entry 1hdp

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protein links
DNA-binding protein PDB id
Protein chain
63 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: Solution structure of a pou-specific homeodomain: 3d-nmr studies of human b-cell transcription factor oct-2
Structure: Oct-2 pou homeodomain. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 1 models
Authors: M.Sivaraja,M.C.Botfield,M.Mueller,A.Jancso,M.A.Weiss
Key ref:
M.Sivaraja et al. (1994). Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2. Biochemistry, 33, 9845-9855. PubMed id: 7914745 DOI: 10.1021/bi00199a005
08-Mar-94     Release date:   26-Jan-95    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09086  (PO2F2_HUMAN) -  POU domain, class 2, transcription factor 2
479 a.a.
63 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1021/bi00199a005 Biochemistry 33:9845-9855 (1994)
PubMed id: 7914745  
Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor Oct-2.
M.Sivaraja, M.C.Botfield, M.Mueller, A.Jancso, M.A.Weiss.
The POU DNA-binding motif defines a conserved family of eukaryotic transcription factors involved in regulation of gene expression. This bipartite motif consists of an N-terminal POU-specific domain (POUs), a flexible linker, and a C-terminal POU-specific homeodomain (POUHD). Here we describe the solution structure of a POU-specific homeodomain. An NMR model is obtained from Oct-2, a human B-cell specific transcription factor which participates in the regulation of immunoglobulin genes. A fragment of Oct-2 containing POUHD and an adjoining linker was expressed in Escherichia coli and characterized by three-dimensional nuclear magnetic resonance (3D-NMR) spectroscopy. Complete 1H and 15N resonance assignment of the POUHD moiety is presented. The POUHD solution structure, as calculated by distance geometry and simulated annealing (DG/SA), is similar to that of canonical homeodomains. A salient difference between solution and crystal structures is observed in the C-terminal segment of alpha-helix 3 (the HTH recognition helix), which is not well ordered in solution. Because this segment presumably folds upon specific DNA binding, its flexibility in solution may reduce the intrinsic DNA affinity of POUHD in the absence of POUs.

Literature references that cite this PDB file's key reference

  PubMed id Reference
16431844 I.Ahmad, D.C.Hoessli, E.Walker-Nasir, S.M.Rafik, A.R.Shakoori, and Nasir-ud-Din (2006).
Oct-2 DNA binding transcription factor: functional consequences of phosphorylation and glycosylation.
  Nucleic Acids Res, 34, 175-184.  
11391564 G.Iurcu-Mustata, D.Van Belle, R.Wintjens, M.Prévost, and M.Rooman (2001).
Role of salt bridges in homeodomains investigated by structural analyses and molecular dynamics simulations.
  Biopolymers, 59, 145-159.  
9852081 J.M.Rhee, C.A.Gruber, T.B.Brodie, M.Trieu, and E.E.Turner (1998).
Highly cooperative homodimerization is a conserved property of neural POU proteins.
  J Biol Chem, 273, 34196-34205.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
  9819426 P.Sauter, and P.Matthias (1998).
Coactivator OBF-1 makes selective contacts with both the POU-specific domain and the POU homeodomain and acts as a molecular clamp on DNA.
  Mol Cell Biol, 18, 7397-7409.  
10384325 W.Herr (1998).
The herpes simplex virus VP16-induced complex: mechanisms of combinatorial transcriptional regulation.
  Cold Spring Harb Symp Quant Biol, 63, 599-607.  
  9144767 H.Li, R.Tejero, D.Monleon, D.Bassolino-Klimas, C.Abate-Shen, R.E.Bruccoleri, and G.T.Montelione (1997).
Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1.
  Protein Sci, 6, 956-970.  
8898894 G.Esposito, F.Fogolari, G.Damante, S.Formisano, G.Tell, A.Leonardi, R.Di Lauro, and P.Viglino (1996).
Analysis of the solution structure of the homeodomain of rat thyroid transcription factor 1 by 1H-NMR spectroscopy and restrained molecular mechanics.
  Eur J Biochem, 241, 101-113.
PDB code: 1ftt
  7613470 E.H.Morita, M.Shirakawa, F.Hayashi, M.Imagawa, and Y.Kyogoku (1995).
Structure of the Oct-3 POU-homeodomain in solution, as determined by triple resonance heteronuclear multidimensional NMR spectroscopy.
  Protein Sci, 4, 729-739.
PDB code: 1ocp
7667096 H.C.van Leeuwen, M.J.Strating, M.Cox, R.Kaptein, and P.C.van der Vliet (1995).
Mutation of the Oct-1 POU-specific recognition helix leads to altered DNA binding and influences enhancement of adenovirus DNA replication.
  Nucleic Acids Res, 23, 3189-3197.  
  7891704 M.A.Cleary, and W.Herr (1995).
Mechanisms for flexibility in DNA sequence recognition and VP16-induced complex formation by the Oct-1 POU domain.
  Mol Cell Biol, 15, 2090-2100.  
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