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- PDB-6tp5: Crystal structure of human Transmembrane prolyl 4-hydroxylase -

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Basic information

Entry
Database: PDB / ID: 6tp5
TitleCrystal structure of human Transmembrane prolyl 4-hydroxylase
ComponentsTransmembrane prolyl 4-hydroxylase
KeywordsOXIDOREDUCTASE / Prolyl-4-hydroxylase / 2-oxoglutarate-binding protein / Transmembrane protein / EF-hand / Double-stranded beta helix / Iron-binding protein / Calcium-binding protein / HIDEA syndrome
Function / homology
Function and homology information


procollagen-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / regulation of erythrocyte differentiation / iron ion binding / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Prolyl 4-hydroxylase / Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / GLYCINE / N-OXALYLGLYCINE / TERTIARY-BUTYL ALCOHOL / Transmembrane prolyl 4-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMyllykoski, M. / Sutinen, A. / Koski, M.K. / Kallio, J.P. / Raasakka, A. / Myllyharju, J. / Wierenga, R.K. / Koivunen, P.
Funding support Finland, 3items
OrganizationGrant numberCountry
Academy of Finland308009 Finland
Jane and Aatos Erkko Foundation Finland
Sigrid Juselius Foundation Finland
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure of transmembrane prolyl 4-hydroxylase reveals unique organization of EF and dioxygenase domains.
Authors: Myllykoski, M. / Sutinen, A. / Koski, M.K. / Kallio, J.P. / Raasakka, A. / Myllyharju, J. / Wierenga, R.K. / Koivunen, P.
History
DepositionDec 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transmembrane prolyl 4-hydroxylase
B: Transmembrane prolyl 4-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,37026
Polymers96,6982
Non-polymers5,67224
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SEC-SAXS results indicate protein is a dimer in solution., light scattering, SLS results indicate molecular weight is between monomer and dimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint54 kcal/mol
Surface area34820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.079, 92.079, 129.500
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transmembrane prolyl 4-hydroxylase / P4H-TM / Hypoxia-inducible factor prolyl hydroxylase 4 / HPH-4


Mass: 48349.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P4HTM, PH4 / Plasmid: pFastBAC Dual / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NXG6, hypoxia-inducible factor-proline dioxygenase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][b-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 155 molecules

#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O
#8: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 62.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Well solution: 0.1 M Tris-HCl pH 9, 22% Tert-butanol, 1 mM N-oxalylglycine Protein solution: 10 mM Tris-HCl pH 7.8, 0.1 M NaCl, 0.1 M Glycine, 2 mM CaCl2, 0.02 mM FeSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.25→50.3 Å / Num. obs: 57041 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.76 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.057 / Rrim(I) all: 0.109 / Net I/σ(I): 7.35
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.95 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4799 / CC1/2: 0.18 / Rpim(I) all: 1.34 / Rrim(I) all: 2.38 / % possible all: 83

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSMar 15, 2019data reduction
XDSMar 15, 2019data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jig

2jig


Resolution: 2.25→50.3 Å / SU ML: 0.3991 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.2415
RfactorNum. reflection% reflection
Rfree0.2213 2008 3.52 %
Rwork0.1815 --
obs0.1829 57031 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.78 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5874 0 366 135 6375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00486374
X-RAY DIFFRACTIONf_angle_d0.69648637
X-RAY DIFFRACTIONf_chiral_restr0.0443978
X-RAY DIFFRACTIONf_plane_restr0.0041092
X-RAY DIFFRACTIONf_dihedral_angle_d9.56524508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.36931040.36713151X-RAY DIFFRACTION77.96
2.31-2.370.37751440.34973923X-RAY DIFFRACTION98.12
2.37-2.440.3411500.32893998X-RAY DIFFRACTION99.88
2.44-2.520.37331420.30793960X-RAY DIFFRACTION99.88
2.52-2.610.32041490.27934028X-RAY DIFFRACTION99.9
2.61-2.710.27231480.24454025X-RAY DIFFRACTION99.86
2.71-2.840.28521460.22553966X-RAY DIFFRACTION99.83
2.84-2.990.28631470.22864029X-RAY DIFFRACTION99.81
2.99-3.170.26241440.20924039X-RAY DIFFRACTION99.9
3.17-3.420.26591510.1933970X-RAY DIFFRACTION99.78
3.42-3.760.21591500.16673982X-RAY DIFFRACTION99.81
3.76-4.30.17471510.14483999X-RAY DIFFRACTION99.28
4.3-5.420.16231500.13723982X-RAY DIFFRACTION99.42
5.42-50.280.18911320.15493971X-RAY DIFFRACTION98.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.097143992590.3945406030550.4139368980232.399777003560.8700846759963.020904179480.0139388683258-0.1180613594370.3101322546160.04645630288440.22490037816-0.381213399349-0.3874078762990.338007985408-0.2132879976140.478715291561-0.1349717886610.08461150443440.41713090614-0.03923423916880.4661854685618.515911598930.9942246763-1.31210523319
27.34636501127-1.346143996753.10490690256.174965554231.18089936587.454311807820.21694191840.5035552047070.0203189224668-0.4354686207680.1203429897270.270807269249-0.0184628588633-0.0537964547516-0.3379729508780.63647842541-0.0181688362633-0.05251355566240.4505898454680.1305448562120.435909974625-10.592821120728.99044746-17.7633061667
34.54419420821-0.03942696077120.1872632904021.72528809230.2657624977821.55543500503-0.01941453353790.05336081475670.59563656666-0.1860761767810.269155656579-0.258523992001-0.4713138443440.321406287353-0.2256279959050.668879986314-0.1084642998210.1191615560660.441704647984-0.08924497281290.57576629236813.637070166438.0232352403-0.939202292186
42.97304719047-0.08405620746-0.6658117241132.192682740650.5366612953122.22645462070.09231640075230.1490235817580.474171840408-0.3378471090310.170769546901-0.347842314422-0.5630817439290.318179584522-0.175895284860.576671347062-0.08946367810450.07528964412090.414499736109-0.03846002388970.50602951061715.940179259331.9538835912-6.51452339482
53.075373808110.584993652572-1.016356473113.21245109976-1.658575832833.67047959831-0.004991795437510.6833583475860.533015814031-0.1818007893360.4174986113050.78045369004-0.198764627163-0.694973120133-0.3304906262040.4707710033920.06437376410960.009342854243290.7091299270840.2178441252310.797201002622-28.84713064823.429993913110.384566444
63.251883753150.136459832918-0.6893408689132.99426910974-0.4537360563724.697579712140.537169366621-0.9034008120350.5964283493590.6243272895960.173279317919-0.0323875434714-0.6315006365050.763781750605-0.4316926354370.756478794062-0.07283020922550.1545385592970.769316516599-0.2065282333990.599304583641-2.2154865950532.975192570624.6485387327
77.4075729345-0.436577419047-2.312751590783.32152686582-0.2291248754152.992306566020.214855170397-0.1104174243621.06897091230.4682441620380.3568819178640.913714088095-0.572554002605-0.666535612223-0.4818505698010.6051203313020.1207603711070.152311174830.5882012199340.2379606914010.935686805253-26.617263909530.981756387815.1356463833
83.023607530180.835098204754-0.6549528095432.56722215501-0.8360473473382.13243898730.114742520995-0.1793843131510.4985769788250.4354010270860.2832992151770.668752770872-0.447190997458-0.337514377344-0.1862005490730.5334235617690.09044035258770.1371339396040.4373209044310.08483340732710.572785605788-22.485299844825.496058216619.7175752304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 107 through 194 )
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 340 )
4X-RAY DIFFRACTION4chain 'A' and (resid 341 through 481 )
5X-RAY DIFFRACTION5chain 'B' and (resid 108 through 189 )
6X-RAY DIFFRACTION6chain 'B' and (resid 190 through 288 )
7X-RAY DIFFRACTION7chain 'B' and (resid 289 through 374 )
8X-RAY DIFFRACTION8chain 'B' and (resid 375 through 481 )

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