The Antennapedia homeodomain protein from Drosophila melanogaster bound to a fragment of DNA (PDB ID 1AHD). Antennapedia is a Hox gene first discovered in Drosophila which controls the placement of Legs A loss-of-function Mutation in the Drosophila melanogaster (from the Greek for black-bellied dew-lover) is a two-winged insect that belongs to the Diptera, the order Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known The recognition helix and unstructured N-terminus are bound in the major and minor grooves respectively.

The homeodomain fold is a protein structural domain that binds DNA or RNA and is thus commonly found in transcription factors. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl A protein domain is a part of protein sequence and structure that can evolve, function and exist independently of the rest of the protein chain Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units In the field of Molecular biology, a transcription factor (sometimes called a sequence-specific DNA binding factor is a Protein that binds to specific sequences The fold consists of a 60-amino acid helix-turn-helix structure in which three alpha helices are connected by short loop regions [1]. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this In Proteins the helix-turn-helix ( HTH) is a major Structural motif capable of binding DNA. A common motif in the Secondary structure of Proteins the alpha helix (α-helix is a right-handed coiled conformation resembling a spring, in which The N-terminal two helices are antiparallel and the longer C-terminal helix is roughly perpendicular to the axes established by the first two. The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or The C-terminus (also known as the carboxyl-terminus, carboxy-terminus, C-terminal end, or It is this third helix that interacts directly with DNA. Homeodomain folds are found exclusively in eukaryotes but have high homology to lambda phage proteins that alter the expression of genes in prokaryotes. Animals Plants fungi, and Protists are eukaryotes (juːˈkærɪɒt or -oʊt Organisms whose cells are organized into complex Enterobacteria phage λ ( Lambda phage) is a temperate bacteriophage that infects Escherichia coli The prokaryotes (proʊˈkærioʊts singular prokaryote /proʊˈkæriət/ are a group of Organisms that lack a Cell nucleus (= karyon or any other In eukaryotes, homeodomains induce cellular differentiation by initiating the cascades of coregulated genes required to produce individual tissues and organs. In Developmental biology, cellular differentiation is the process by which a less specialized cell becomes a more specialized Cell type. Tissue is a cellular organizational level intermediate between cells and a complete organism In Biology, an organ ( Latin: organum, "instrument tool" from Greek όργανον - organon "organ instrument

Homeobox genes

Further information: Homeobox

Homeobox genes are stretches of DNA about 180 nucleotides long that code for homeodomain proteins in both vertebrates and invertebrates. A homeobox is a DNA sequence found within Genes that are involved in the regulation of patterns of development ( Morphogenesis) in Animals Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group Vertebrates are members of the Subphylum Vertebrata, Chordates with backbones or spinal columns The grouping sometimes includes An invertebrate is an Animal lacking a Vertebral column. The group includes 98% of all animal Species — all animals except those in the Chordate The existence of homeoboxes was first discovered in Drosophila, where the radical alterations that resulted from mutations in homeobox genes were termed homeotic mutations. Drosophila is a Genus of small flies, belonging to the family Drosophilidae, whose members are often called "fruit flies" The most famous such mutation is Antennapedia, in which legs grow from the head of a fly instead of the expected antennae. Antennapedia is a Hox gene first discovered in Drosophila which controls the placement of Legs A loss-of-function Mutation in the Homeobox genes are thus critical in the establishment of body axes during embryogenesis. Embryogenesis is the process by which the Embryo is formed and develops

Sequence specificity

Homeodomains can bind both specifically and nonspecifically to B-DNA with the C-terminal recognition helix aligning in the DNA's major groove and the unstructured peptide "tail" at the N-terminus aligning in the minor groove. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known The recognition helix and the inter-helix loops are rich in arginine and lysine residues, which form hydrogen bonds to the DNA backbone; conserved hydrophobic residues in the center of the recognition helix aid in stabilizing the helix packing. Arginine (abbreviated as Arg or R) is an α- Amino acid. The L-form is one of the 20 most common natural amino acids Lysine (abbreviated as Lys or K) is an α- Amino acid with the Chemical formula HO2CCH(NH2(CH24NH2 A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen Conservation refers to a high degree of similarity in orthologous DNA sequences protein sequences, or Protein structures amongst various In Chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of Homeodomain proteins show a preference for the DNA sequence 5'-ATTA-3'; sequence-independent binding occurs with significantly lower affinity.

POU proteins

Proteins containing a POU region consist of a homeodomain and a separate, structurally homologous POU domain that contains two helix-turn-helix motifs and also binds DNA. In Proteins the helix-turn-helix ( HTH) is a major Structural motif capable of binding DNA. The two domains are linked by a flexible loop that is long enough to stretch around the DNA helix, allowing the two domains to bind on opposite sides of the target DNA, collectively covering an eight-base segment with consensus sequence 5'-ATGCAAAT-3'. In Molecular biology and Bioinformatics, a consensus sequence is a way of representing the results of a multiple Sequence alignment, where related sequences The individual domains of POU proteins bind DNA only weakly, but have strong sequence-specific affinity when linked. Interestingly, the POU domain itself has significant structural similarity with repressors expressed in bacteriophages, particularly lambda phage. This article is about a biological infectious particle for other uses see Phage (disambiguation. Enterobacteria phage λ ( Lambda phage) is a temperate bacteriophage that infects Escherichia coli

References

1. Branden C, Tooze J. (1999). Introduction to Protein Structure 2nd ed. Garland Publishing: New York, NY. (See especially pp159-66. )