1APL | pdb_00001apl

CRYSTAL STRUCTURE OF A MAT-ALPHA2 HOMEODOMAIN-OPERATOR COMPLEX SUGGESTS A GENERAL MODEL FOR HOMEODOMAIN-DNA INTERACTIONS

• PDB DOI: https://doi.org/10.2210/pdb1APL/pdb
• NAKB: 1APL

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1993-10-04 Released: 1993-10-21 
• Deposition Author(s): Wolberger, C., Vershon, A.K., Liu, B., Johnson, A.D., Pabo, C.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work: 
  0.226 (Depositor) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions.

Wolberger, C., Vershon, A.K., Liu, B., Johnson, A.D., Pabo, C.O.

(1991) Cell 67: 517-528

• PubMed: 1682054 
• DOI: https://doi.org/10.1016/0092-8674(91)90526-5
• Primary Citation Related Structures: 
  1APL


• PubMed Abstract: 
  

  The MAT alpha 2 homeodomain regulates the expression of cell type-specific genes in yeast. We have determined the 2.7 A resolution crystal structure of the alpha 2 homeodomain bound to a biologically relevant DNA sequence. The DNA in this complex is contacted primarily by the third of three alpha-helices, with additional contacts coming from an N-terminal arm. Comparison of the yeast alpha 2 and the Drosophila engrailed homeodomain-DNA complexes shows that the protein fold is highly conserved, despite a 3-residue insertion in alpha 2 and only 27% sequence identity between the two homeodomains. Moreover, the orientation of the recognition helix on the DNA is also conserved. This docking arrangement is maintained by side chain contacts with the DNA--primarily the sugar-phosphate backbone--that are identical in alpha 2 and engrailed. Since these residues are conserved among all homeodomains, we propose that the contacts with the DNA are also conserved and suggest a general model for homeodomain-DNA interactions.

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Organizational Affiliation: 
• Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.43 kDa 
• Atom Count: 1,791 
• Modeled Residue Count: 159 
• Deposited Residue Count: 208 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (MAT-ALPHA2 HOMEODOMAIN)	C, D	83	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: MAT ALPHA2 RES. 128-210
UniProt
Find proteins for P0CY08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CY08  Go to UniProtKB:  P0CY08

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*CP*AP*TP*GP*TP*AP*AP*TP*TP*CP*AP*TP*TP*TP*AP*C P*AP*CP*GP*C)-3')	A	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*GP*TP*GP*TP*AP*AP*AP*TP*GP*AP*AP*TP*TP*A P*CP*AP*TP*G)-3')	B	21	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Work:  0.226 (Depositor) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.78	α = 90
b = 39.93	β = 97.35
c = 68.79	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-21 
Deposition Author(s): Wolberger, C., Vershon, A.K., Liu, B., Johnson, A.D., Pabo, C.O.

Revision History  

• Version 1.0: 1993-10-21
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references