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- PDB-5jtc: Aspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR dom... -

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Basic information

Entry
Database: PDB / ID: 5jtc
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH)oxygenase and TPR domains in complex with manganese, 2,4-pyridine dicarboxylate and factor X substrate peptide fragment(39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor X
KeywordsOXIDOREDUCTASE / 2-oxoglutarate dependent oxygenase / aspartyl/asparaginyl beta-hydroxylase / EGF-like domain hydroxylase / double stranded beta-helix / tetratricopeptide repeat
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / : / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum ...peptide-aspartate beta-dioxygenase / : / regulation of protein depolymerization / activation of store-operated calcium channel activity / regulation of cell communication by electrical coupling / junctional sarcoplasmic reticulum membrane / peptidyl-aspartic acid 3-dioxygenase activity / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum / positive regulation of intracellular protein transport / coagulation factor Xa / pattern specification process / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / face morphogenesis / structural constituent of muscle / response to ATP / roof of mouth development / Protein hydroxylation / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / positive regulation of TOR signaling / detection of calcium ion / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium ion homeostasis / Intrinsic Pathway of Fibrin Clot Formation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / regulation of protein stability / phospholipid binding / Golgi lumen / calcium ion transmembrane transport / Stimuli-sensing channels / blood coagulation / transmembrane transporter binding / electron transfer activity / cell population proliferation / positive regulation of cell migration / endoplasmic reticulum lumen / negative regulation of cell population proliferation / serine-type endopeptidase activity / external side of plasma membrane / calcium ion binding / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Tetratricopeptide repeat / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / TPR repeat region circular profile. / Epidermal growth factor-like domain. / TPR repeat profile. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Tetratricopeptide-like helical domain superfamily / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / : / PYRIDINE-2,4-DICARBOXYLIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsMcDonough, M.A. / Pfeffer, I.
CitationJournal: Sci Rep / Year: 2020
Title: Aspartate/asparagine-beta-hydroxylase: a high-throughput mass spectrometric assay for discovery of small molecule inhibitors.
Authors: Brewitz, L. / Tumber, A. / Pfeffer, I. / McDonough, M.A. / Schofield, C.J.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Jan 10, 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Coagulation factor X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9906
Polymers53,5962
Non-polymers3944
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.020, 91.660, 123.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Aspartyl/asparaginyl beta-hydroxylase / Aspartate beta-hydroxylase / ASP beta-hydroxylase / Peptide-aspartate beta-dioxygenase


Mass: 49405.336 Da / Num. of mol.: 1 / Fragment: UNP Residues 330-758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPH, BAH / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q12797, peptide-aspartate beta-dioxygenase
#2: Protein/peptide Coagulation factor X / Stuart factor / Stuart-Prower factor


Mass: 4190.384 Da / Num. of mol.: 1 / Fragment: UNP Residues 86-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00742, coagulation factor Xa

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Non-polymers , 5 types, 220 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PD2 / PYRIDINE-2,4-DICARBOXYLIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG3350, 200mM NaBr, 100mM BisTris Propane, 1mM MnCl2, 2mM 2,4-PDCA, 330uM ASPH, 726uM Factor X

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.24→91.66 Å / Num. obs: 28029 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 30.589 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.031 / Net I/σ(I): 19.8
Reflection shellResolution: 2.24→2.3 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_2386refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQY

5jqy


Resolution: 2.24→73.508 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.12
RfactorNum. reflection% reflection
Rfree0.2085 1407 5.03 %
Rwork0.1812 --
obs0.1826 27971 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 48.1335 Å2 / Biso min: 17.87 Å2
Refinement stepCycle: final / Resolution: 2.24→73.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 20 216 3815
Biso mean--37.99 46.23 -
Num. residues----447
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)
10.15220.0494-0.95353.20773.90094.96540.30810.1186-0.0928-0.0682-0.17180.16780.0954-0.1375-0.12230.40730.1354-0.1230.3475-0.01570.422865.293732.376450.1982
23.2241-0.29381.90821.84880.15744.13620.0863-0.448-0.16060.25680.07470.02880.397-0.5824-0.08730.2246-0.07920.0050.31430.01830.208453.773619.340916.4908
36.9463-0.80446.04121.8325-0.79777.7591-0.11970.6390.03840.43180.202-0.1895-0.23510.3343-0.01660.28480.0325-0.02860.6041-0.04820.427862.1824.892427.2402
41.51772.79180.61195.4455-0.326.7361-0.394-1.42021.21590.20920.2930.5994-0.3711-0.39370.12190.78240.243-0.18320.9074-0.29080.611455.162831.598236.6373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 330 through 537 )A330 - 537
2X-RAY DIFFRACTION2chain 'A' and (resid 538 through 758 )A538 - 758
3X-RAY DIFFRACTION3chain 'B' and (resid 99 through 108 )B99 - 108
4X-RAY DIFFRACTION4chain 'B' and (resid 109 through 116 )B109 - 116

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