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1.14.11.2: procollagen-proline 4-dioxygenase

This is an abbreviated version!
For detailed information about procollagen-proline 4-dioxygenase, go to the full flat file.

Word Map on EC 1.14.11.2

Reaction

Procollagen L-proline
+
2-oxoglutarate
 +
O2
=
procollagen trans-4-hydroxy-L-proline
 +
succinate
 +
CO2

Synonyms

A085R, alpha (I) subunit, anthrax-P4H, AT-P4H-1, At-P4H-2, BaP4H, C-P4H, C-P4H alpha subunit (III), C-P4H alpha(I), C-P4H alpha(III), CePHY-1/PHY-2/PDI2, collagen proline hydroxylase, collagen prolyl 4-hydroxylase, collagen prolyl 4-hydroxylase (type-II), collagen prolyl 4-hydroxylase 1, collagen prolyl-4-hydroxylase, collagen prolyl-4-hydroxylase alpha subunit 2, CP4H, CP4H1, CrP4H-1, DmP4H, egg-laying abnormal-9 prolyl hydroxylase, Egl nine homolog, EGLN, EGLN prolyl hydroxylase, EGLN3, EGLN3 hydroxylase, GBAA_4459, HIF prolyl hydroxylase, HIF prolyl-4-hydroxylase, HIF-1alpha-specific prolyl-hydroxylase, HIF-P4H-1, HIF-P4H-2, HIF-P4H-3, HPH, HPH-2, HuPH4-I, HuPH4-II, hydroxylase, collagen proline, hypoxia inducible factor prolyl-4-hydroxylase domain-containing protein, hypoxia inducible factor-prolyl hydroxylase, hypoxia-inducible factor -1alpha-type prolyl 4-hydroxylase, hypoxia-inducible factor prolyl hydroxylase, hypoxia-inducible factor-1alpha-prolyl-hydroxylase 2, More, NtP4H1.1, P4H, P4H alpha1, P4H-1, P4H1, P4ha1, P4ha2, P4Halpha(I), P4Halpha(II), P4Halpha(III), P4Halpha1, PBCV-1 P4H, peptidyl proline hydroxylase, PH, PHD, PHD-1, PHD1, PHD2, PHD3, procollagen prolyl 4-hydroxylase, procollagen-proline dioxygenase, proline 4-hydroxylase, proline hydroxylase, proline protocollagen hydroxylase, proline, 2-oxoglutarate dioxygenase, proline,2-oxoglutarate 4-dioxygenase, prolyl 4-hydroxylase, prolyl 4-hydroxylase A085R, prolyl hydroxylase, prolyl hydroxylase domain 1, prolyl hydroxylase domain containing protein, prolyl hydroxylase domain enzyme, prolyl hydroxylase domain protein 2, prolyl hydroxylase-1, prolyl hydroxylase-3, prolyl-4-hydroxylase, prolyl-4-hydroxylase alpha I, prolyl-4-hydroxylase alpha II, prolyl-4-hydroxylase alpha subunit 2, prolyl-4-hydroxylase alpha1, prolyl-4-hydroxylase-alpha1, prolyl-4-hydroxylases, prolyl-glycyl-peptide, 2-oxoglutarate:oxygen oxidoreductase, 4-hydroxylating, prolyl4-hydroxylase, prolylprotocollagen dioxygenase, prolylprotocollagen hydroxylase, protocollagen hydroxylase, protocollagen proline 4-hydroxylase, protocollagen proline dioxygenase, protocollagen proline hydroxylase, protocollagen prolyl hydroxylase, PSB-II, Skp1 prolyl hydroxylase, type I C-P4H, type I proly 4-hydroxylase, type I proyl 4-hydroxylase, type II proyl 4-hydroxylase

ECTree

     1 Oxidoreductases
         1.14 Acting on paired donors, with incorporation or reduction of molecular oxygen
             1.14.11 With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
                1.14.11.2 procollagen-proline 4-dioxygenase

Crystallization

Crystallization on EC 1.14.11.2 - procollagen-proline 4-dioxygenase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme BaP4H complexed with cadmium or 2-oxoglutarate, mixing of 0.001 ml of 9 mg/ml protein solution containing 1 mM CoCl2 and 1 mM 2-oxoglutarate with 0.001 ml of reservoir solution containing 0.1 M HEPES, pH 7.8, 0.05 M cadmium sulfate, and 0.9 M sodium acetate, equilibration against 0.35 ml of reservoir solution, at 20°C, X-ray diffraction structure determination and analysis at 1.63 and 2.35 A resolution, respectively, soaking of the different crystals in different cryoprotection solutions, molecular replacement using the monomer (chain A), PDB Id 3itq, as a starting model
Q81LZ8
purified recombinant apoenzyme in complex with inhibitor malonate and Co2+, hanging drop vapor diffusion, mixing of 0.001 ml of a solution of 9 mg/ml protein, 1 mM CoCl2, and 1 mM L-Pro, with 0.001 ml of reservoir solution containing 0.1 M malonate/imidazole/boric acid, pH 6.5, and 18% PEG 1500, 2 days, or purified recombinant apoenzyme BaP4H with (P-P-G)3 peptide fused to the C terminus and Co2+, sitting drop vapor diffusion, mixing of 0.001 ml of 12 mg/ml protein solution containing 1 mM CoCl2, and 1 mM 2-oxoglutarate, with 0.001 ml of reservoir solution containing 0.15 M KBr and 30% PEG 2000 MME, 20°C, method optimization, X-ray diffraction structure determination and analysis, molecular replacement for apo-BaP4H using structure PDB ID 3ITQ as a starting model. Models for Co(II)-BaP4H-MLI and Co(II)-BaP4H-PPG are obtained by molecular replacement with the apo-BaP4H structure
Q81LZ8
purified SeMet anthrax P4H, hanging drop vapor diffusion method, 24 mg/mL protein in 50 mM Tris, pH 7.4, containing 150 mM KCl and 5 mM 2-mercaptoethanol, is mixed with and equal volume of well solution containing 16% w/v PEG 8000, 40 mM potassium phosphate, pH 4.0-4.2, and 20% v/v glycerol, at 20°C, under aerobic conditions, 1-2 weeks, X-ray diffraction structure determination and analysis at 1.4 A resolution
Q81LZ8
recombinant selenomethionine-labeled anthrax-P4H, hanging-drop vapor-diffusion method, 0.001 ml of 24 mg/ml recombinant protein in 50 mM Tris-HCl, 150 mM KCl, and 5 mM 2-mercaptoethanol, pH 7.4, is mixed with 0.001 ml and equilibrated against 0.75 ml of reservoir solution containing 16% w/v PEG 8000, 40 mM potassium phosphate, and 20% glycerol at 20°C, X-ray diffraction structure determination and analysis at 1.4 A resolution, molecular replacement
-
purifed recombinant detagged enzyme in ternary complex with Zn2+ and substrate (Ser-Pro)5 peptide, 3 mg/ml protein in 0.01 M Tris-HCl, 0.1 M NaCl, 0.1 M glycine, pH 7.8, 5 mM ZnSO4, 2 mM pyridine 2,4-dicarboxylate, and 2.5 mM (Ser-Pro)5, mixed with precipitant solution contains a 5% w/v polyethylene glycol mixture with equal amounts of PEG 400, PEG 1000, PEG 1500, PEG 4000, PEG 6000, PEG 8000, PEG MME 550, PEG MME 750, and PEG MME 5000 in 0.1 M acetate, pH 5.5, and 10 mM zinc acetate, 22°C, 1 week, X-ray diffraction structure determination and analysis at 1.98 A resolution
-
structures of apoenzyme at 1.93 and 2.90 A resolution, complexed with the competitive inhibitor Zn2+, and with Zn2+ and pyridine 2,4-dicarboxylate at 1.85 A resolution. The structures reveal the double-stranded alpha-helix core fold typical for 2-oxoglutarate dioxygenases. The catalytic site is at the center of an extended shallow groove lined by two flexible loops
-
crystal structures of the PSB domain of the human C-P4H isoform II (PSB-II) complexed with and without various short proline-rich peptides are described
hanging drop vapour diffusion method
-
hanging-drop vapour diffusion, 0.002 ml of 10 mg/ml protein solution in 20 mM bis-Tris, 100 mM glycine, pH 6.8 is mixed with 0.002 ml reservoir solution containing 1.2-1.7 M ammonium phosphate, pH 8.2-8.6, crystals diffract to 3.0 A
-
recombinant catalytic domain of PHD2 in complex with the C-terminal oxygen-dependent degradation domain of HIF-1alpha, 20°C, 100 nl protein solution containing 40 mg/ml protein in 50 mM Tris-HCl, pH 7.5, 1 mM MnCl2, 1 mM NOG, and 0.1 mM HIF-1alpha CODD556-574 mixed with 100 nl of well solution consisting of 0.2 M MgCl2 and 20% PEG 3350, A tPHD2-Fe2+-B-CODD568-574 crystal is obtained by soaking preformed PHD2181-426-Fe2+-B crystals in 50% sodium malonate, pH 7.5, solution containing 10 mM 4R-hydroxylated Pro564 HIF-1alpha CODD556-574(Hyp564) peptide under anaerobic conditions for 72 h. The PHD2-Fe2+-inhibitor complexes crystallize in an apparently homotrimeric form, method optimization, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement
-
sitting-drop vapor diffusion method