PDBsum entry 3a02

Gene regulation

PDB id

3a02

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Contents

			Protein chain

					51 a.a. *

			Metals

					_CL


					_CD

			Waters ×99

* Residue conservation analysis

PDB id:

3a02

Links

Name:

Gene regulation

Title:

Crystal structure of aristaless homeodomain

Structure:

Homeobox protein aristaless. Chain: a. Fragment: homeobox, residues 91-146. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: al, cg3935. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.00Å

R-factor:

0.173

R-free:

0.184

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

	Headers

	References

Protein chain

Q06453 (AL_DROME) - Homeobox protein aristaless from Drosophila melanogaster

Seq: Struc:					408 a.a. 51 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	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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