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PDBsum entry 3a01

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protein dna_rna Protein-protein interface(s) links
Gene regulation/DNA PDB id
3a01
Jmol
Contents
Protein chains
78 a.a. *
57 a.a. *
68 a.a. *
61 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
3a01
Name: Gene regulation/DNA
Title: Crystal structure of aristaless and clawless homeodomains bo
Structure: Homeodomain-containing protein. Chain: a, e. Fragment: clawless homeobox, residues 170-261. Engineered: yes. Homeobox protein aristaless. Chain: b, f. Fragment: homeobox, residues 80-146. Engineered: yes. 5'-d( Gp Gp Cp Tp Tp Ap Ap Tp Tp Ap Ap Tp Tp Gp C
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: c15, cg7937. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: al, cg3935. Synthetic: yes. Synthetic: yes
Resolution:
2.70Å     R-factor:   0.234     R-free:   0.283
Authors: K.Miyazono,K.Nagata,K.Saigo,T.Kojima,M.Tanokura
Key ref: K.Miyazono et al. (2010). Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless. EMBO J, 29, 1613-1623. PubMed id: 20389279
Date:
28-Feb-09     Release date:   09-Mar-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9VD99  (Q9VD99_DROME) -  Homeodomain-containing protein
Seq:
Struc:
307 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
Q06453  (AL_DROME) -  Homeobox protein aristaless
Seq:
Struc:
408 a.a.
57 a.a.
Protein chain
Pfam   ArchSchema ?
Q9VD99  (Q9VD99_DROME) -  Homeodomain-containing protein
Seq:
Struc:
307 a.a.
68 a.a.
Protein chain
Pfam   ArchSchema ?
Q06453  (AL_DROME) -  Homeobox protein aristaless
Seq:
Struc:
408 a.a.
61 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 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  

 

 
EMBO J 29:1613-1623 (2010)
PubMed id: 20389279  
 
 
Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.
K.Miyazono, Y.Zhi, Y.Takamura, K.Nagata, K.Saigo, T.Kojima, M.Tanokura.
 
  ABSTRACT  
 
To achieve accurate gene regulation, some homeodomain proteins bind cooperatively to DNA to increase those site specificities. We report a ternary complex structure containing two homeodomain proteins, aristaless (Al) and clawless (Cll), bound to DNA. Our results show that the extended conserved sequences of the Cll homeodomain are indispensable to cooperative DNA binding. In the Al-Cll-DNA complex structure, the residues in the extended regions are used not only for the intermolecular contacts between the two homeodomain proteins but also for the sequence-recognition mechanism of DNA by direct interactions. The residues in the extended N-terminal arm lie within the minor groove of DNA to form direct interactions with bases, whereas the extended conserved region of the C-terminus of the homeodomain interacts with Al to stabilize and localize the third alpha helix of the Cll homeodomain. This structure suggests a novel mode for the cooperativity of homeodomain proteins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21106075 R.Torella, E.Moroni, M.Caselle, G.Morra, and G.Colombo (2010).
Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes.
  BMC Struct Biol, 10, 42.  
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