2HDD

ENGRAILED HOMEODOMAIN Q50K VARIANT DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history


Literature

Engrailed (Gln50-->Lys) homeodomain-DNA complex at 1.9 A resolution: structural basis for enhanced affinity and altered specificity.

Tucker-Kellogg, L.Rould, M.A.Chambers, K.A.Ades, S.E.Sauer, R.T.Pabo, C.O.

(1997) Structure 5: 1047-1054

  • DOI: 10.1016/s0969-2126(97)00256-6
  • Primary Citation of Related Structures:  
    2HDD

  • PubMed Abstract: 
  • The homeodomain is one of the key DNA-binding motifs used in eukaryotic gene regulation, and homeodomain proteins play critical roles in development. The residue at position 50 of many homeodomains appears to determine the differential DNA-binding specificity, helping to distinguish among binding sites of the form TAATNN ...

    The homeodomain is one of the key DNA-binding motifs used in eukaryotic gene regulation, and homeodomain proteins play critical roles in development. The residue at position 50 of many homeodomains appears to determine the differential DNA-binding specificity, helping to distinguish among binding sites of the form TAATNN. However, the precise role(s) of residue 50 in the differential recognition of alternative sites has not been clear. None of the previously determined structures of homeodomain-DNA complexes has shown evidence for a stable hydrogen bond between residue 50 and a base, and there has been much discussion, based in part on NMR studies, about the potential importance of water-mediated contacts. This study was initiated to help clarify some of these issues.


    Organizational Affiliation

    Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge 02139, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ENGRAILED HOMEODOMAIN Q50K)C [auth A], D [auth B]61Drosophila melanogasterMutation(s): 1 
Gene Names: enCG9015
UniProt
Find proteins for P02836 (Drosophila melanogaster)
Explore P02836 
Go to UniProtKB:  P02836
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*C P*CP*GP*GP*A)-3')A [auth C]21N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*G P*CP*AP*AP*A)-3')B [auth D]21N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  2HDD Kd: 8.80e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.72α = 90
b = 45.34β = 119.53
c = 72.47γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance