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PDBsum entry 1lfb

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protein links
Transcription regulation PDB id
1lfb
Jmol
Contents
Protein chain
78 a.a. *
* Residue conservation analysis
PDB id:
1lfb
Name: Transcription regulation
Title: The x-ray structure of an atypical homeodomain present in the rat liver transcription factor lfb1(slash)hnf1 and implications for DNA binding
Structure: Liver transcription factor (lfb1). Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: liver
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.212     R-free:   0.364
Authors: T.A.Ceska,M.Lamers,P.Monaci,A.Nicosia,R.Cortese,D.Suck
Key ref: T.A.Ceska et al. (1993). The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding. EMBO J, 12, 1805-1810. PubMed id: 8491173
Date:
28-Jun-93     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15257  (HNF1A_RAT) -  Hepatocyte nuclear factor 1-alpha
Seq:
Struc:
 
Seq:
Struc:
628 a.a.
78 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

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

 

 
EMBO J 12:1805-1810 (1993)
PubMed id: 8491173  
 
 
The X-ray structure of an atypical homeodomain present in the rat liver transcription factor LFB1/HNF1 and implications for DNA binding.
T.A.Ceska, M.Lamers, P.Monaci, A.Nicosia, R.Cortese, D.Suck.
 
  ABSTRACT  
 
The transcription factor LFB1/HNF1 from rat liver nuclei is a 628 amino acid protein that functions as a dimer binding to the inverted palindrome GTTAATN-ATTAAC consensus site. We have crystallized a 99 residue protein containing the homeodomain portion of LFB1, and solved its structure using X-ray diffraction data to 2.8 A resolution. The topology and orientation of the helices is essentially the same as that found in the engrailed, MAT alpha 2 and Antennapedia homeodomains, even though the LFB1 homeodomain contains 21 more residues. The 21 residue insertion is found in an extension of helix 2 and consequent lengthening of the connecting loop between helix 2 and helix 3. Comparison with the engrailed homeodomain-DNA complex indicates that the mode of interaction with DNA is similar in both proteins, with a number of conserved contacts in the major groove. The extra 21 residues of the LFB1 homeodomain are not involved in DNA binding. Binding of the LFB1 dimer to a B-DNA palindromic consensus sequence requires either a conformational change of the DNA (presumably bending), or a rearrangement of the subunits relative to the DNA.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20157477 R.T.Moreland, J.F.Ryan, C.Pan, and A.D.Baxevanis (2009).
The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family.
  Database (Oxford), 2009, bap004.  
17306756 J.Lee, and S.Safe (2007).
Coactivation of estrogen receptor alpha (ER alpha)/Sp1 by vitamin D receptor interacting protein 150 (DRIP150).
  Arch Biochem Biophys, 461, 200-210.  
15625066 J.E.Lee, K.Kim, J.C.Sacchettini, C.V.Smith, and S.Safe (2005).
DRIP150 coactivation of estrogen receptor alpha in ZR-75 breast cancer cells is independent of LXXLL motifs.
  J Biol Chem, 280, 8819-8830.  
15837198 M.S.Yousef, and B.W.Matthews (2005).
Structural basis of Prospero-DNA interaction: implications for transcription regulation in developing cells.
  Structure, 13, 601-607.
PDB code: 1xpx
12520008 S.Banerjee-Basu, T.Moreland, B.J.Hsu, K.L.Trout, and A.D.Baxevanis (2003).
The Homeodomain Resource: 2003 update.
  Nucleic Acids Res, 31, 304-306.  
12429095 J.M.Ryter, C.Q.Doe, and B.W.Matthews (2002).
Structure of the DNA binding region of prospero reveals a novel homeo-prospero domain.
  Structure, 10, 1541-1549.
PDB code: 1mij
12453420 Y.I.Chi, J.D.Frantz, B.C.Oh, L.Hansen, S.Dhe-Paganon, and S.E.Shoelson (2002).
Diabetes mutations delineate an atypical POU domain in HNF-1alpha.
  Mol Cell, 10, 1129-1137.
PDB code: 1ic8
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.  
11470884 S.Banerjee-Basu, and A.D.Baxevanis (2001).
Molecular evolution of the homeodomain family of transcription factors.
  Nucleic Acids Res, 29, 3258-3269.  
11125116 S.Banerjee-Basu, D.W.Sink, and A.D.Baxevanis (2001).
The Homeodomain Resource: sequences, structures, DNA binding sites and genomic information.
  Nucleic Acids Res, 29, 291-293.  
10592263 S.Banerjee-Basu, J.F.Ryan, and A.D.Baxevanis (2000).
The homeodomain resource: a prototype database for a large protein family.
  Nucleic Acids Res, 28, 329-330.  
10585442 M.Vaxillaire, A.Abderrahmani, P.Boutin, B.Bailleul, P.Froguel, M.Yaniv, and M.Pontoglio (1999).
Anatomy of a homeoprotein revealed by the analysis of human MODY3 mutations.
  J Biol Chem, 274, 35639-35646.  
10502778 S.Banerjee-Basu, and A.D.Baxevanis (1999).
Threading analysis of the Pitx2 homeodomain: predicted structural effects of mutations causing Rieger syndrome and iridogoniodysgenesis.
  Hum Mutat, 14, 312-319.  
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.  
9881151 M.Hertzberg, and O.Olsson (1998).
Molecular characterisation of a novel plant homeobox gene expressed in the maturing xylem zone of Populus tremula x tremuloides.
  Plant J, 16, 285-295.  
9092652 D.J.Sourdive, C.Transy, S.Garbay, and M.Yaniv (1997).
The bifunctional DCOH protein binds to HNF1 independently of its 4-alpha-carbinolamine dehydratase activity.
  Nucleic Acids Res, 25, 1476-1484.  
  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.  
9336443 T.R.Bürglin (1997).
Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals.
  Nucleic Acids Res, 25, 4173-4180.  
8702862 A.Zhu, and M.A.Kuziora (1996).
Homeodomain interaction with the beta subunit of the general transcription factor TFIIE.
  J Biol Chem, 271, 20993-20996.  
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
8972866 S.A.Kuznetsova, C.Clusel, E.Ugarte, I.Elias, M.Vasseur, M.Blumenfeld, and Z.A.Shabarova (1996).
Crosslinking of double-stranded oligonucleotides containing O-methyl-substituted pyrophosphate groups to the HNF1 transcription factor in nuclear cell extract.
  Nucleic Acids Res, 24, 4783-4790.  
8749853 D.Frishman, and P.Argos (1995).
Knowledge-based protein secondary structure assignment.
  Proteins, 23, 566-579.  
7739902 D.L.Smith, A.B.Desai, and A.D.Johnson (1995).
DNA bending by the a1 and alpha 2 homeodomain proteins from yeast.
  Nucleic Acids Res, 23, 1239-1243.  
  7744010 R.Ficner, U.H.Sauer, G.Stier, and D.Suck (1995).
Three-dimensional structure of the bifunctional protein PCD/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1.
  EMBO J, 14, 2034-2042.  
7907417 J.K.Tyler, K.E.Allen, and R.D.Everett (1994).
Mutation of a single lysine residue severely impairs the DNA recognition and regulatory functions of the VZV gene 62 transactivator protein.
  Nucleic Acids Res, 22, 270-278.  
7909177 T.R.Bürglin (1994).
A Caenorhabditis elegans prospero homologue defines a novel domain.
  Trends Biochem Sci, 19, 70-71.  
8044836 W.J.Gehring, Y.Q.Qian, M.Billeter, K.Furukubo-Tokunaga, A.F.Schier, D.Resendez-Perez, M.Affolter, G.Otting, and K.Wüthrich (1994).
Homeodomain-DNA recognition.
  Cell, 78, 211-223.  
8374950 R.G.Brennan (1993).
The winged-helix DNA-binding motif: another helix-turn-helix takeoff.
  Cell, 74, 773-776.  
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.