ELM Details - LIG

LIG_HOMEOBOX

Functional site class:	Homeodomain ligand
Functional site description:	The YPWM motif in HOX proteins confers binding to PBX homeobox domains.
ELM(s):	LIG_HOMEOBOX
LIG_HOMEOBOX description:	The Homeobox (Hox) family consists of a large number of transcription factors which have a vital role in development of the embryo in determining the anterior/posterior and rosto/caudal axis in multicellular organisms. Hox proteins share a conserved 60 amino-acid region; homeodomain, PMID: 7979246, which has specific DNA binding activity, and promotes regulation of multiple target genes. The YPWM functional site, PMID: 1359544, is found in several Hox proteins and is located N-terminal in respect to the homeodomain, and acts as a ligand to the extended Pbx homeodomain, forming a hetrodimer. This interaction increases the DNA binding affinity of the Hox proteins containing the YPWM functional site. The structure suggests, PMID:12409300 & PDB: 1LFU, a lock and key mechanism where the YPWM motif engages in an interaction in a hydrophobic pocket located in the extended Pbx homeodomain.
Pattern:	[FY][DEP]WM
Present in taxon(s):	Metazoa
Not represented in taxon(s):

See instances for LIG_HOMEOBOX

Abstract

The YPWM motif in HOX proteins confers binding to PBX homeodomains.

Selected references

Passner JM, Ryoo HD, Shen L, Mann RS, Aggarwal AK

Structure of a DNA-bound Ultrabithorax-Extradenticle homeodomain complex.

Nature 1999 Feb 25;397(6721) : 714-9.

PMID: 10067897

Sprules T, Green N, Featherstone M, Gehring K

Lock and key binding of the HOX YPWM peptide to the PBX homeodomain.

J Biol Chem 2003 Jan 10;278(2) : 1053-8.

PMID: 12409300

This ELM has been assigned the following Gene Ontology (GO) terms for biological process, cellular component and molecular function.

Biological Process

  embryonic development

GO:0009790

  pattern specification

GO:0007389

Cellular Component

  nucleus

GO:0005634

Molecular Function

  transcription regulator

GO:0030528

Instances for LIG_HOMEOBOX

Sequence	Position	Subsequence (Click for evidence information)	PDB	Gene Name	Protein Description	Organism
HXD4_HUMAN	134-137	QPAVVYPWMKKVHVN	-	Name=HOXD4; Synonyms=HOX4B;	Homeobox protein Hox-D4 (Hox-4B) (Hox-5.1) (HHO.C13).	Homo sapiens (Human).
CDX1_HUMAN	133-136	QRPTPYEWMRRSVAA	-	Name=CDX1;	Homeobox protein CDX-1 (Caudal-type homeobox protein 1).	Homo sapiens (Human).
HXA1_HUMAN	205-208	SPAQTFDWMKVKRNP	-	Name=HOXA1; Synonyms=HOX1F;	Homeobox protein Hox-A1 (Hox-1F).	Homo sapiens (Human).
HXB1_HUMAN	180-183	PTARTFDWMKVKRNP	-	Name=HOXB1; Synonyms=HOX2I;	Homeobox protein Hox-B1 (Hox-2I).	Homo sapiens (Human).
HXB2_HUMAN	95-98	PPAPEFPWMKEKKSA	-	Name=HOXB2; Synonyms=HOX2H;	Homeobox protein Hox-B2 (Hox-2H) (Hox-2.8) (K8).	Homo sapiens (Human).
HXB3_HUMAN	130-133	LTKQIFPWMKESRQT	-	Name=HOXB3; Synonyms=HOX2G;	Homeobox protein Hox-B3 (Hox-2G) (Hox-2.7).	Homo sapiens (Human).
HXB4_HUMAN	142-145	KEPVVYPWMRKVHVS	-	Name=HOXB4; Synonyms=HOX2F;	Homeobox protein Hox-B4 (Hox-2F) (Hox-2.6).	Homo sapiens (Human).
HXB5_HUMAN	177-180	QTPQIFPWMRKLHIS	-	Name=HOXB5; Synonyms=HOX2A;	Homeobox protein Hox-B5 (Hox-2A) (HHO.C10) (HU-1).	Homo sapiens (Human).
HXB6_HUMAN	128-131	CSTPVYPWMQRMNSC	-	Name=HOXB6; Synonyms=HOX2B;	Homeobox protein Hox-B6 (Hox-2B) (Hox-2.2) (HU-2).	Homo sapiens (Human).
HXB7_HUMAN	127-130	SNFRIYPWMRSSGTD	-	Name=HOXB7; Synonyms=HOX2C;	Homeobox protein Hox-B7 (Hox-2C) (HHO.C1).	Homo sapiens (Human).
HXB8_HUMAN	135-138	SPTQLFPWMRPQAAA	-	Name=HOXB8; Synonyms=HOX2D;	Homeobox protein Hox-B8 (Hox-2D) (Hox-2.4).	Homo sapiens (Human).
HXC8_HUMAN	139-142	SPSLMFPWMRPHAPG	-	Name=HOXC8; Synonyms=HOX3A;	Homeobox protein Hox-C8 (Hox-3A).	Homo sapiens (Human).
PDX1_HUMAN	119-122	RVQLPFPWMKSTKAH	-	Name=PDX1; Synonyms=IPF1;	Pancreas/duodenum homeobox protein 1 (PDX-1) (Insulin promoter factor 1) (IPF-1) (Islet/duodenum homeobox-1) (IDX-1) (Somatostatin- transactivating factor 1) (STF-1) (Insulin upstream factor 1) (IUF-1) (Glucose-sensitive factor) (GSF).	Homo sapiens (Human).
TLX1_HUMAN	174-177	LTGLTFPWMESNRRY	-	Name=TLX1; Synonyms=HOX11, TCL3;	T-cell leukemia homeobox protein 1 (Homeobox protein Hox-11) (T-cell leukemia/lymphoma protein 3) (Proto-oncogene TCL-3).	Homo sapiens (Human).
TLX2_HUMAN	118-121	LAGLTFPWMDSGRRF	-	Name=TLX2; Synonyms=HOX11L1, NCX;	T-cell leukemia homeobox protein 2 (Homeobox protein Hox-11L1) (Neural crest homeobox protein).	Homo sapiens (Human).
TLX3_HUMAN	125-128	LGGLNFPWMESSRRF	-	Name=TLX3; Synonyms=HOX11L2;	T-cell leukemia homeobox protein 3 (Homeobox protein Hox-11L2).	Homo sapiens (Human).