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 

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This is version 1.4 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: https://doi.org/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). 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ENGRAILED HOMEODOMAINC [auth A],
D [auth B]
57Drosophila melanogasterMutation(s): 1 
UniProt
Find proteins for P02836 (Drosophila melanogaster)
Explore P02836 
Go to UniProtKB:  P02836
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02836
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
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
Sequence Annotations
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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
  • Version 1.3: 2021-11-03
    Changes: Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection