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- PDB-6yyw: Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR do... -

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Basic information

Entry
Database: PDB / ID: 6yyw
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor XFactor X
KeywordsOXIDOREDUCTASE / Aspartyl/asparaginyl beta-hydroxylase / Dioxygenase
Function / homology
Function and homology information


peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis ...peptide-aspartate beta-dioxygenase / regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity / 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 / cortical endoplasmic reticulum / sarcoplasmic reticulum lumen / limb morphogenesis / coagulation factor Xa / pattern specification process / positive regulation of intracellular protein transport / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / activation of cysteine-type endopeptidase activity / face morphogenesis / Extrinsic Pathway of Fibrin Clot Formation / structural constituent of muscle / positive regulation of calcium ion transport into cytosol / response to ATP / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / positive regulation of TOR signaling / calcium ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / Intrinsic Pathway of Fibrin Clot Formation / muscle contraction / calcium ion transmembrane transport / phospholipid binding / regulation of protein stability / Stimuli-sensing channels / Golgi lumen / blood coagulation / cell population proliferation / transmembrane transporter binding / electron transfer activity / positive regulation of cell migration / negative regulation of cell population proliferation / external side of plasma membrane / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / 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 / 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 ...Aspartyl beta-hydroxylase/Triadin domain / Aspartyl/asparaginyl beta-hydroxylase family / Aspartyl beta-hydroxylase N-terminal region / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / 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-type aspartate/asparagine hydroxylation site / EGF-like domain / 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. / TPR repeat profile. / Epidermal growth factor-like domain. / Tetratricopeptide repeats / Tetratricopeptide repeat / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Tetratricopeptide-like helical domain superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2020
Title: Synthesis of 2-oxoglutarate derivatives and their evaluation as cosubstrates and inhibitors of human aspartate/asparagine-beta-hydroxylase.
Authors: Brewitz, L. / Nakashima, Y. / Schofield, C.J.
History
DepositionMay 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)53,7974
Polymers53,5962
Non-polymers2012
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-15 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.439, 90.951, 123.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 49405.336 Da / Num. of mol.: 1
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 / Factor X / Stuart factor / Stuart-Prower factor


Mass: 4190.384 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: synthetic construct (others) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 55.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Bis Tris Propane, 200 mM sodium acetate trihydrate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 2-oxoglutarate, 18 mg/ml protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.27→29.64 Å / Num. obs: 26364 / % possible obs: 97.2 % / Redundancy: 12.6 % / Biso Wilson estimate: 45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Net I/σ(I): 12
Reflection shellResolution: 2.27→2.34 Å / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1700 / CC1/2: 0.807 / % possible all: 69.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTC

5jtc


Resolution: 2.27→29.64 Å / SU ML: 0.286 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1051
RfactorNum. reflection% reflection
Rfree0.2237 1999 7.6 %
Rwork0.1875 --
obs0.1902 26297 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.89 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 0 143 3710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01433660
X-RAY DIFFRACTIONf_angle_d1.5144943
X-RAY DIFFRACTIONf_chiral_restr0.0599518
X-RAY DIFFRACTIONf_plane_restr0.0089646
X-RAY DIFFRACTIONf_dihedral_angle_d22.96151374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.330.3399860.33981052X-RAY DIFFRACTION60.47
2.33-2.390.30611450.27811755X-RAY DIFFRACTION99.84
2.39-2.460.32281440.25721747X-RAY DIFFRACTION100
2.46-2.540.29591440.24131765X-RAY DIFFRACTION99.95
2.54-2.630.25271460.23141761X-RAY DIFFRACTION100
2.63-2.730.31861440.2381761X-RAY DIFFRACTION99.9
2.73-2.860.25421450.22721766X-RAY DIFFRACTION99.9
2.86-3.010.27841470.20951775X-RAY DIFFRACTION99.9
3.01-3.20.23651450.22171770X-RAY DIFFRACTION100
3.2-3.440.24431460.19711777X-RAY DIFFRACTION100
3.44-3.790.19671480.17191795X-RAY DIFFRACTION100
3.79-4.340.19481500.16021817X-RAY DIFFRACTION100
4.34-5.460.17931500.1461825X-RAY DIFFRACTION100
5.46-29.640.19181590.1621932X-RAY DIFFRACTION99.9

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