PDBsum entry 1san

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protein links
DNA-binding protein PDB id
Protein chain
62 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA-binding protein
Title: The des(1-6)antennapedia homeodomain: comparison of the nmr solution structure and the DNA binding affinity with the intact antennapedia homeodomain
Structure: Antennapedia protein. Chain: a. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Organ: fruit. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 20 models
Authors: Y.Q.Qian,D.Resendez-Perez,W.J.Gehring,K.Wuthrich
Key ref: Y.Q.Qian et al. (1994). The des(1-6)antennapedia homeodomain: comparison of the NMR solution structure and the DNA-binding affinity with the intact Antennapedia homeodomain. Proc Natl Acad Sci U S A, 91, 4091-4095. PubMed id: 7909611 DOI: 10.1073/pnas.91.9.4091
07-Jan-94     Release date:   30-Apr-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02833  (ANTP_DROME) -  Homeotic protein antennapedia
378 a.a.
62 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     transcription regulatory region sequence-specific DNA binding     4 terms  


DOI no: 10.1073/pnas.91.9.4091 Proc Natl Acad Sci U S A 91:4091-4095 (1994)
PubMed id: 7909611  
The des(1-6)antennapedia homeodomain: comparison of the NMR solution structure and the DNA-binding affinity with the intact Antennapedia homeodomain.
Y.Q.Qian, D.Resendez-Perez, W.J.Gehring, K.Wüthrich.
The nuclear magnetic resonance (NMR) solution structure of an N-terminally truncated mutant Antennapedia homeodomain, des(1-6)Antp(C39S), has been determined from 935 nuclear Overhauser effect upper distance constraints and 148 dihedral angle constraints by using the programs DIANA and OPAL. Twenty conformers representing the solution structure of des(1-6)Antp(C39S) have an average root-mean-square distance relative to the mean coordinates of 0.56 A for the backbone atoms of residues 8-59. Comparison with the intact Antp(C39S) homeodomain shows that the two proteins have identical molecular architectures. The removal of the N-terminal residues 1-6, which are flexibly disordered in the intact homeodomain, causes only strictly localized structure variations and does not noticeably affect the adjoining helix I from residues 10-21. The DNA-binding constant of des(1-6)Antp(C39S) is approximately 10-fold reduced relative to the intact Antp(C39S) homeodomain, which can now be attributed to the absence of the previously reported contacts of the N-terminal polypeptide segment of the intact Antp(C39S) homeodomain with the minor groove of the DNA duplex.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18562673 J.Favor, C.J.Gloeckner, A.Neuhäuser-Klaus, W.Pretsch, R.Sandulache, S.Saule, and I.Zaus (2008).
Relationship of Pax6 activity levels to the extent of eye development in the mouse, Mus musculus.
  Genetics, 179, 1345-1355.  
10933814 T.Sprules, N.Green, M.Featherstone, and K.Gehring (2000).
Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides.
  Biochemistry, 39, 9943-9950.
PDB code: 1du6
9837817 I.McIntosh, S.D.Dreyer, M.V.Clough, J.A.Dunston, W.Eyaid, C.M.Roig, T.Montgomery, S.Ala-Mello, I.Kaitila, A.Winterpacht, B.Zabel, M.Frydman, W.G.Cole, C.A.Francomano, and B.Lee (1998).
Mutation analysis of LMX1B gene in nail-patella syndrome patients.
  Am J Hum Genet, 63, 1651-1658.  
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.  
  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.  
8943030 T.E.Haerry, and W.J.Gehring (1996).
Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila.
  Proc Natl Acad Sci U S A, 93, 13884-13889.  
  8557047 J.A.Hirsch, and A.K.Aggarwal (1995).
Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.
  EMBO J, 14, 6280-6291.
PDB code: 1jgg
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