6yw0 | pdb_00006yw0

Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287

spinqualitylabelsall models 6yw0, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6yw0 is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 2JP, BCT, FE NonStd Res: MLY Related: 4bqw, 4bqx, 4bqy, 6yvw, 6yvx, 6yvz Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 (HUMAN) Activity: Hypoxia-inducible factor-proline dioxygenase, with EC number 1.14.11.29 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Disease [EGLN1_HUMAN] Defects in EGLN1 are the cause of familial erythrocytosis type 3 (ECYT3) [MIM:609820]. ECYT3 is an autosomal dominant disorder characterized by increased serum red blood cell mass, elevated serum hemoglobin and hematocrit, and normal serum erythropoietin levels. Function [EGLN1_HUMAN] Cellular oxygen sensor that catalyzes, under normoxic conditions, the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. Hydroxylates a specific proline found in each of the oxygen-dependent degradation (ODD) domains (N-terminal, NODD, and C-terminal, CODD) of HIF1A. Also hydroxylates HIF2A. Has a preference for the CODD site for both HIF1A and HIF1B. Hydroxylated HIFs are then targeted for proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Under hypoxic conditions, the hydroxylation reaction is attenuated allowing HIFs to escape degradation resulting in their translocation to the nucleus, heterodimerization with HIF1B, and increased expression of hypoxy-inducible genes. EGLN1 is the most important isozyme under normoxia and, through regulating the stability of HIF1, involved in various hypoxia-influenced processes such as angiogenesis in retinal and cardiac functionality. Publication Abstract from PubMed Crystallization is the bottleneck in macromolecular crystallography; even when a protein crystallises, crystal packing often influences ligand-binding and protein-protein interaction interfaces, which are the key points of interest for functional and drug discovery studies. The human hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) readily crystallises as a homotrimer, but with a sterically blocked active site. We explored strategies aimed at altering PHD2 crystal packing by protein modification and molecules that bind at its active site and elsewhere. Following the observation that, despite weak inhibition/binding in solution, succinamic acid derivatives readily enable PHD2 crystallization, we explored methods to induce crystallization without active site binding. Cyclic peptides obtained via mRNA display bind PHD2 tightly away from the active site. They efficiently enable PHD2 crystallization in different forms, both with/without substrates, apparently by promoting oligomerization involving binding to the C-terminal region. Although our work involves a specific case study, together with those of others, the results suggest that mRNA display-derived cyclic peptides may be useful in challenging protein crystallization cases. Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.,Chowdhury R, Abboud MI, McAllister TE, Banerji B, Bhushan B, Sorensen JL, Kawamura A, Schofield CJ Sci Rep. 2020 Dec 15;10(1):21964. doi: 10.1038/s41598-020-76307-8. PMID:33319810 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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