The Eukaryotic Linear Motif resource for
Functional Sites in Proteins
Functional site class:
Hydroxyproline modification in hypoxia signaling
Functional site description:
In normoxia, a site in Hypoxia-induced factor (Hif-1) is hydroxylated by prolyl hydroxylases and recognized by von Hippel-Lindau tumor suppressor protein (VHL) which leads to ubiquitination and proteasomal degradation. Under hypoxic conditions, the site is not hydroxylated and thus the protein is not degraded.
ELM Description:
The motif of oxygen dependent prolyl hydroxylation is often depicted as LxxLAP. However, that consensus may be misleading as it does not correspond to known interaction preferences. The motif entered in ELM is based on the pVHL interacting residues in the complex with the hydroxylated peptide and their equivalent in vertebrates, fly and worm. It finds a third match in Hif2 alpha in addition to the two experimental motifs
Pattern: [IL]A(P).{6,8}[FLIVM].[FLIVM]
Pattern Probability: 0.0000704
Present in taxons: Caenorhabditis elegans Drosophila melanogaster Homo sapiens Metazoa Mus musculus
Interaction Domain:
VHL (PF01847) von Hippel-Lindau disease tumour suppressor protein (Stochiometry: 1 : 1)
PDB Structure: 1LQB
o See 8 Instances for DEG_ODPH_VHL_1
o Abstract
Cells respond to decreased oxygen with the induction of an adaptive gene expression programme aimed at restoring oxygen supply and maintaining cell viability during oxygen restriction. Most of the genes induced during low oxygen exposure are under control of the hypoxia inducible factor. The transcription factor Hif-1 (hypoxia-inducible factor 1) plays an essential role in the maintenance of oxygen homeostasis in metazoan organisms. It is a heterodimer composed of an oxygen regulated Hif-1 alpha subunit and a constituvely expressed Hif-1 beta subunit. Under normoxic conditions, Hif-1 alpha is continuously synthesized and degraded, while under hypoxic conditions it accumulates, dimerizes with Hif-1 beta and activates its target gene transcription. In normoxia, Hif-1 alpha is hydroxylated at P402 and P564 (human numbering) by prolyl hydroxylases. This allows binding of von Hippel-Lindau protein (pVHL) which leads to ubiquitination and proteosomal degradation of the Hif-1 alpha . Under hypoxic conditions, hydroxylase activity is reduced due to substrate limitation, inhibition of the catalytic centre or both, this leads to accumulation of Hif-1 alpha which can enter the nucleus, dimerize with Hif-1 beta and activate transcription of hypoxic genes. Activated genes include erythropoietin, glucose transporters, glycolytic enzymes, vascular endothelial growth factor, and others whose protein products increase oxygen delivery or facilitate metabolic adaptation to hypoxia. Hif-1 alpha is often over expressed in the majority of common human cancers and their metastases, due to the presence of intratumoral hypoxia and as a result of mutation in genes encoding oncoproteins and tumor suppressors. Solid tumors require vascularization and so the hypoxia pathway is seen as a major therapeutic target.
Three isoforms of Hif alpha (Hif-1 alpha, Hif-2 alpha and Hif-3 alpha) are encoded by distinct genetic loci. Sites from all isoforms align into a conserved LxxLAP motif. This sequence is evolutionarily conserved in Hif alpha proteins from nematodes to mammals (11292861). However, several studies suggest the absence of a rigid consensus sequence for binding of Hypoxia-inducible factor prolyl hydroxylases (Huang,2002; Li,2004). Also, it was shown that downstream residue L574 is required for prolyl hydroxylation and binding of Hif-prolyl hydroxylase 2 (Kageyama,2004). Moreover, the X-ray structure of the complex between Hif-1 alpha peptide bound to pVHL reveals a bipartite binding site, namely, residues 560-567 that include hydroxylated P564 and residues 571-577 that include L574 (1LM8 and 1LQB) (Min,2002; Hon,2002). Two other proteins were also suggested to have the LxxLAP motif. I-kappa-B kinase-beta (IKK beta) protein contains an evolutionarily conserved LxxLAP sequence on a loop of its protein kinase domain. It was suggested that hypoxia releases repression of NF-kappa-B activity through prolyl-hydroxylase dependent hydroxylation of IKK beta. The second protein is the Rpb1 subunit of RNA polymerase II. It was reported that pVHL specifically binds the hyperphosphorylated Rpb1 in a proline-hydroxylation-dependent manner, targeting it for ubiquitination. These finding are difficult to reconcile with the enzymatic studies of prolyl hydroxylase specificity cited above. It is possible that only the Hif1 proteins will prove to have the hypoxia hydroxyproline modification site.
o 7 selected references:

o 7 GO-Terms:

o 8 Instances for DEG_ODPH_VHL_1
(click table headers for sorting; Notes column: =Number of Switches, =Number of Interactions)
Acc., Gene-, NameStartEndSubsequenceLogic#Ev.OrganismNotes
Q99814 EPAS1
574 585 IFQPLAPVAPHSPFLLDKFQ TP 1 Homo sapiens (Human)
Q99814 EPAS1
529 542 LETLAPYIPMDGEDFQLSPI TP 1 Homo sapiens (Human)
Q99814 EPAS1
403 416 LAQLAPTPGDAIISLDFGNQ TP 1 Homo sapiens (Human)
G5EGD2 hif-1
619 631 LSCLAPFVDTYDMMQMDEGL TP 1 Caenorhabditis elegans
490 502 LEMLAPYISMDDDFQLNASE TP 2 Homo sapiens (Human)
Q24167 sima
1173 1184 NGASIAPVNTKATIRLVESK TP 1 Drosophila melanogaster (Fruit fly)
Q16665 HIF1A
562 574 LEMLAPYIPMDDDFQLRSFD TP 3 Homo sapiens (Human)
Q16665 HIF1A
400 413 LTLLAPAAGDTIISLDFGSN TP 1 Homo sapiens (Human)
Please cite: ELM 2016-data update and new functionality of the eukaryotic linear motif resource. (PMID:26615199)

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