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InterPro: IPR009057 Homeodomain-like

Protein matches Help

UniProtKB

Matches:

88440 proteins

Overview:	sorted by AC,	sorted by name,	of known structure,	proteins with splice variants
Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
Table:	For all matching proteins,	of known structure
Architectures
Accession List
Matches in BioMart

Accession

IPR009057 Homeodomain-like

Type

Domain

Signatures Help

Database	ID	Name	Proteins
SuperFamily	SSF46689	Homeodomain_like	88440
Signatures in BioMart

InterPro Relationships Help

Children

IPR006120 Resolvase, helix-turn-helix domain
IPR012287 Homeodomain-related
IPR014875 Mor transcription activator

Found in

IPR000747 Homeobox engrailed
IPR002492 Transposase, Tc1/Tc3
IPR002514 Transposase IS3/IS911
IPR002622 Transposase, Synechocystis PCC 6803
IPR003022 Transcription factor Otx2
IPR003025 Transcription factor Otx
IPR003220 Insertion element protein
IPR004906 Transposase, Tc5
IPR005412 DNA-binding protein Fis
IPR010113 Nif-specific regulatory protein
IPR010114 Signal transduction response regulator, nitrogen regulation NR(I)
IPR011526 Helix-turn-helix, Psq-like
IPR011785 Transcriptional regulator PpsR
IPR012704 Signal transduction response regulator, propionate catabolism, transcriptional regulator PrpR
IPR014264 Signal transduction response regulator, PEP-CTERM system, putative
IPR014317 Transcription activator PspF
IPR016233 Homeobox Pitx/unc30
IPR017894 Helix-turn-helix, IS21 transposase-type
IPR018060 Helix-turn-helix, AraC domain
IPR019915 Transcriptional regulator, pyrimidine utilisation, RutR

Contains

IPR000047 Helix-turn-helix motif, lambda-like repressor
IPR002197 Helix-turn-helix, Fis-type
IPR006600 Centromere protein Cenp-B, helix-turn-helix domain
IPR014778 Myb, DNA-binding
IPR015175 Centromere protein Cenp-B, DNA-binding domain 2
IPR015280 Rap1, DNA-binding
IPR017930 HTH transcriptional regulator, Myb-type, DNA-binding
IPR017970 Homeobox, conserved site
IPR019737 Homeobox engrailed-type, conserved site
IPR020441 Helix-turn-helix, Fis
IPR020479 Homeobox, region

InterPro annotation

Entry Details in BioMart

Abstract

Homeodomain proteins are transcription factors that share a related DNA binding homeodomain [1]. The homeodomain was first identified in a number of Drosophila homeotic and segmentation proteins, but is now known to be well conserved in many other animals, including vertebrates. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA. The first helix helps to stabilise the structure. Many proteins contain homeodomains, including Drosophila Engrailed, yeast mating type proteins, hepatocyte nuclear factor 1a and HOX proteins.

The homeodomain motif is very similar in sequence and structure to domains in a wide range of DNA-binding proteins, including recombinases, Myb proteins, GARP response regulators, human telomeric proteins (hTRF1), paired domain proteins (PAX), yeast RAP1, centromere-binding proteins CENP-B and ABP-1, transcriptional regulators (TyrR), AraC-type transcriptional activators, and tetracycline repressor-like proteins (TetR, QacR, YcdC) [2, 3, 4].

Structural links Help

PDB - click here

SCOP: a.121.1.1 , a.4.1.1 , a.4.1.11 , a.4.1.12 , a.4.1.13 , a.4.1.14 , a.4.1.2 , a.4.1.3 , a.4.1.4 , a.4.1.5 , a.4.1.6 , a.4.1.7 , a.4.1.8 , a.4.1.9 , b.82.4.1 , g.48.1.1 , i.11.1.1 , j.92.1.1

CATH: 1.10.10.10 , 1.10.10.500 , 1.10.10.60 , 1.10.1680.10 , 1.10.260.40 , 1.10.357.10 , 1.10.8.60 , 3.40.10.10

Interactions Help

This domain has been experimentally proven to be involved in Protein:Protein interactions.
Representative data is shown with the following example proteins:

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR009057

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

O08755 Hepatocyte nuclear factor 6

O14529 Homeobox protein cut-like 2

P01366 Mating-type protein A1

P02833 Homeotic protein antennapedia

P34257 Transposable element Tc3 transposase

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR020479	Homeobox, region
IPR017995	Homeobox protein, antennapedia type
IPR001827	Homeobox protein, antennapedia type, conserved site
IPR012287	Homeodomain-related
IPR017970	Homeobox, conserved site
IPR002492	Transposase, Tc1/Tc3
IPR003350	Homeodomain protein CUT
IPR001356	Homeobox
IPR009057	Homeodomain-like
	PDB Chain
	ModBase
	CATH Domain
	SWISS-MODEL
	SCOP Domain

Publications Open in usermanual
1.	Mannervik M. Target genes of homeodomain proteins. Bioessays 21 267-70 1999 [PubMed: 10377888] http://dx.doi.org/10.1002/(SICI)1521-1878(199904)21:4<267::AID-BIES1>3.3.CO;2-3
2.	Hosoda K, Imamura A, Katoh E, Hatta T, Tachiki M, Yamada H, Mizuno T, Yamazaki T. Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. Plant Cell 14 2015-29 2002 [PubMed: 12215502] http://dx.doi.org/10.1105/tpc.002733
3.	Nishikawa T, Nagadoi A, Yoshimura S, Aimoto S, Nishimura Y. Solution structure of the DNA-binding domain of human telomeric protein, hTRF1. Structure 6 1057-65 1998 [PubMed: 9739097] http://dx.doi.org/10.1016/S0969-2126(98)00106-3
4.	Kisker C, Hinrichs W, Tovar K, Hillen W, Saenger W. The complex formed between Tet repressor and tetracycline-Mg2+ reveals mechanism of antibiotic resistance. J. Mol. Biol. 247 260-80 1995 [PubMed: 7707374] http://dx.doi.org/10.1006/jmbi.1994.0138

Additional Reading Open in usermanual
	Joly N, Rappas M, Buck M, Zhang X. Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride. J. Mol. Biol. 375 2008 1206-11 [PubMed: 18082766] http://dx.doi.org/10.1016/j.jmb.2007.11.050
	Peters KM, Schuman JT, Skurray RA, Brown MH, Brennan RG, Schumacher MA. QacR-cation recognition is mediated by a redundancy of residues capable of charge neutralization. Biochemistry 47 2008 8122-9 [PubMed: 18616285] http://dx.doi.org/10.1021/bi8008246
	Palm GJ, Lederer T, Orth P, Saenger W, Takahashi M, Hillen W, Hinrichs W. Specific binding of divalent metal ions to tetracycline and to the Tet repressor/tetracycline complex. J. Biol. Inorg. Chem. 13 2008 1097-110 [PubMed: 18548290] http://dx.doi.org/10.1007/s00775-008-0395-2
	Aleksandrov A, Schuldt L, Hinrichs W, Simonson T. Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study. J. Mol. Biol. 378 2008 898-912 [PubMed: 18395746] http://dx.doi.org/10.1016/j.jmb.2008.03.022
	Zhang F, Gonzalez A, Zhao M, Payne CT, Lloyd A. A network of redundant bHLH proteins functions in all TTG1-dependent pathways of Arabidopsis. Development 130 2003 4859-69 [PubMed: 12917293] http://dx.doi.org/10.1242/dev.00681
	Ko S, Jun SH, Bae H, Byun JS, Han W, Park H, Yang SW, Park SY, Jeon YH, Cheong C, Kim WT, Lee W, Cho HS. Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins. Nucleic Acids Res. 36 2008 2739-55 [PubMed: 18367475] http://dx.doi.org/10.1093/nar/gkn030
	Rubin E, Wu X, Zhu T, Cheung JC, Chen H, Lorincz A, Pandita RK, Sharma GG, Ha HC, Gasson J, Hanakahi LA, Pandita TK, Sukumar S. A role for the HOXB7 homeodomain protein in DNA repair. Cancer Res. 67 2007 1527-35 [PubMed: 17308091] http://dx.doi.org/10.1158/0008-5472.CAN-06-4283

InterPro 23.1