1DU0

ENGRAILED HOMEODOMAIN Q50A VARIANT DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploring the role of glutamine 50 in the homeodomain-DNA interface: crystal structure of engrailed (Gln50 --> ala) complex at 2.0 A.

Grant, R.A.Rould, M.A.Klemm, J.D.Pabo, C.O.

(2000) Biochemistry 39: 8187-8192

  • DOI: 10.1021/bi000071a
  • Primary Citation of Related Structures:  
    1DU0

  • PubMed Abstract: 
  • We have determined the crystal structure of a complex containing the engrailed homeodomain Gln50 --> Ala variant (QA50) bound to the wild-type optimal DNA site (TAATTA) at 2.0 A resolution. Biochemical and genetic studies by other groups have suggested that residue 50 is an important determinant of differential DNA-binding specificity among homeodomains (distinguishing among various sites of the general form TAATNN) ...

    We have determined the crystal structure of a complex containing the engrailed homeodomain Gln50 --> Ala variant (QA50) bound to the wild-type optimal DNA site (TAATTA) at 2.0 A resolution. Biochemical and genetic studies by other groups have suggested that residue 50 is an important determinant of differential DNA-binding specificity among homeodomains (distinguishing among various sites of the general form TAATNN). However, biochemical studies of the QA50 variant had revealed that it binds almost as tightly as the wild-type protein and with only modest changes in specificity. We have now determined the crystal structure of the QA50 variant to help understand the role of residue 50 in site-specific recognition. Our cocrystal structure shows some interesting changes in the water structure at the site of the substitution and shows some changes in the conformations of neighboring side chains. However, the structure, like the QA50 biochemical data, suggests that Gln50 plays a relatively modest role in determining the affinity and specificity of the engrailed homeodomain.


    Related Citations: 
    • Engrailed homeodomain-DNA complex at 2.2 Angstroms resolution: A detailed view of the interface and comparison with other engrailed structures
      Fraenkel, E., Rould, M.A., Chambers, K.A., Pabo, C.O.
      (1998) J Mol Biol 284: 351
    • Engrailed (gln50->lys) homeodomain-DNA complex at 1.9 Angstroms resolution: structural basis for enhanced affinity and altered specificity
      Tucker-Kellogg, L., Rould, M.A., Chambers, K.A., Ades, S.E., Sauer, R.T.
      (1997) Structure 5: 1047
    • Differential DNA-binding specificity of the engrailed homeodomain: the role of residue 50
      Ades, S.E., Sauer, R.T.
      (1994) Biochemistry 33: 9187
    • Crystal structure of an engrailed homeodomain-DNA comples at 2.8 Angstroms resolution: a framework for understanding homeodomain-DNA interactions
      Kissinger, C.A., Liu, B., Martin-Blanco, E., Kornberg, T.B., Pabo, C.O.
      (1990) Cell 63: 579

    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ENGRAILED HOMEODOMAINC [auth A], D [auth B]57Drosophila 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*TP*AP*CP*CP*TP*AP*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*TP*AP*GP*GP*TP*AP*AP*TP*TP*AP*CP*AP*TP*GP*GP*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:  1DU0 Kd: 0.08 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.9α = 90
b = 45.55β = 119.9
c = 71.62γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance