The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Homeodomain ligand
Functional site description:
The YPWM motif in HOX proteins confers binding to PBX homeobox domains.
ELM 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, which has specific DNA binding activity, and promotes regulation of multiple target genes (Gehring,1994). The YPWM functional site, is found in several Hox proteins and is located N-terminal in respect to the homeodomain (Qian,1992), 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. Structural data (1LFU; Sprules,2003) suggest 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
Pattern Probability: 9.953e-07
Present in taxon: Metazoa
Interaction Domain:
Homeobox (PF00046) Homeobox domain (Stochiometry: 1 : 1)
PDB Structure: 1B72
o See 16 Instances for LIG_HOMEOBOX
o Abstract
The YPWM motif in HOX proteins confers binding to PBX homeodomains.
o 2 selected references:

o 4 GO-Terms:

o 16 Instances for LIG_HOMEOBOX
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
P09629 HOXB7
127 130 AAESNFRIYPWMRSSGTDRK TP 1 Homo sapiens (Human)
O43711 TLX3
125 128 VSSLGGLNFPWMESSRRFVK TP 1 Homo sapiens (Human)
O43763 TLX2
118 121 AGGLAGLTFPWMDSGRRFAK TP 1 Homo sapiens (Human)
P31314 TLX1
174 177 VNNLTGLTFPWMESNRRYTK TP 1 Homo sapiens (Human)
P52945 PDX1
119 122 EPNRVQLPFPWMKSTKAHAW TP 1 Homo sapiens (Human)
P09016 HOXD4
134 137 ALKQPAVVYPWMKKVHVNSV TP 1 Homo sapiens (Human)
P17481 HOXB8
135 138 QSPSPTQLFPWMRPQAAAGR TP 1 Homo sapiens (Human)
P17509 HOXB6
128 131 EQKCSTPVYPWMQRMNSCNS TP 1 Homo sapiens (Human)
P09067 HOXB5
177 180 PEGQTPQIFPWMRKLHISHD TP 1 Homo sapiens (Human)
P17483 HOXB4
142 145 SACKEPVVYPWMRKVHVSTV TP 1 Homo sapiens (Human)
P14651 HOXB3
130 133 NSTLTKQIFPWMKESRQTSK TP 1 Homo sapiens (Human)
P14652 HOXB2
95 98 PAAPPAPEFPWMKEKKSAKK TP 1 Homo sapiens (Human)
P14653 HOXB1
180 183 PNTPTARTFDWMKVKRNPPK TP 2 Homo sapiens (Human)
P49639 HOXA1
205 208 ETSSPAQTFDWMKVKRNPPK TP 1 Homo sapiens (Human)
P47902 CDX1
133 136 PGAQRPTPYEWMRRSVAAGG TP 1 Homo sapiens (Human)
P31273 HOXC8
139 142 QNSSPSLMFPWMRPHAPGRR TP 1 Homo sapiens (Human)
Please cite: The Eukaryotic Linear Motif resource: 2022 release. (PMID:34718738)

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