1puf

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1puf, resolution 1.90Å (default scene)
Gene:	HOXA9 (Mus musculus), PBX1 (Homo sapiens)
Structural annotation: Resources: CATH : 1Pufa00, 1Pufb00 InterPro : Ipr000047, Ipr001356, Ipr012287, Ipr009057, Ipr006711, Ipr005542 Pfam : PF00046 SCOP : d1pufa_, d1pufb_ UniProt : P09631, P40424
Functional annotation: Cellular component: nucleus cytoplasm Biological process: regulation of transcription, DNA-dependent multicellular organismal development transcription regulation of transcription C21-steroid hormone biosynthetic process regulation of transcriptional preinitiation complex assembly embryonic development transcription from RNA polymerase II promoter cell differentiation hindbrain development sex differentiation Molecular function: DNA binding protein binding transcription activator activity transcription factor activity sequence-specific DNA binding
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA

Publication Abstract from PubMed

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The HOX/HOM superfamily of homeodomain proteins controls cell fate and segmental embryonic patterning by a mechanism that is conserved in all metazoans. The linear arrangement of the Hox genes on the chromosome correlates with the spatial distribution of HOX protein expression along the anterior-posterior axis of the embryo. Most HOX proteins bind DNA cooperatively with members of the PBC family of TALE-type homeodomain proteins, which includes human Pbx1. Cooperative DNA binding between HOX and PBC proteins requires a residue N-terminal to the HOX homeodomain termed the hexapeptide, which differs significantly in sequence between anterior- and posterior-regulating HOX proteins. We report here the 1.9-A-resolution structure of a posterior HOX protein, HoxA9, complexed with Pbx1 and DNA, which reveals that the posterior Hox hexapeptide adopts an altered conformation as compared with that seen in previously determined anterior HOX/PBC structures. The additional nonspecific interactions and altered DNA conformation in this structure account for the stronger DNA-binding affinity and altered specificity observed for posterior HOX proteins when compared with anterior HOX proteins. DNA-binding studies of wild-type and mutant HoxA9 and HoxB1 show residues in the N-terminal arm of the homeodomains are critical for proper DNA sequence recognition despite lack of direct contact by these residues to the DNA bases. These results help shed light on the mechanism of transcriptional regulation by HOX proteins and show how DNA-binding proteins may use indirect contacts to determine sequence specificity.

Structure of HoxA9 and Pbx1 bound to DNA: Hox hexapeptide and DNA recognition anterior to posterior., LaRonde-LeBlanc NA, Wolberger C, Genes Dev. 2003 Aug 15;17(16):2060-72. PMID:12923056

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1puf is a 4 chain structure with sequence from Homo sapiens and Mus musculus. Full crystallographic information is available from OCA.

See Also

• Tomato aspermy virus protein 2b Suppression of RNA Silencing
• User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing

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