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

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Basic information

Entry
Database: PDB / ID: 6yyx
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 3-methyl-2-oxoglutarate, and factor X substrate peptide fragment(39mer-4Ser)
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor 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 / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum ...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 / sarcoplasmic reticulum lumen / limb morphogenesis / cortical endoplasmic reticulum / 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 / response to ATP / positive regulation of calcium ion transport into cytosol / roof of mouth development / positive regulation of ryanodine-sensitive calcium-release channel activity / Protein hydroxylation / positive regulation of proteolysis / detection of calcium ion / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of TOR signaling / 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 / calcium ion homeostasis / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / muscle contraction / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / Intrinsic Pathway of Fibrin Clot Formation / cellular response to calcium ion / calcium ion transmembrane transport / regulation of protein stability / Stimuli-sensing channels / phospholipid binding / Golgi lumen / blood coagulation / transmembrane transporter binding / cell population proliferation / electron transfer activity / positive regulation of cell migration / negative regulation of cell population proliferation / endoplasmic reticulum lumen / external side of plasma membrane / 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 ...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-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. / TPR repeat profile. / Epidermal growth factor-like domain. / Tetratricopeptide repeats / EGF-like domain profile. / Tetratricopeptide repeat / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / 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 / Tetratricopeptide-like helical domain superfamily / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / Chem-Q1Z / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsNakashima, Y. / Brewitz, L. / Schofield, C.J.
CitationJournal: Chem Sci / Year: 2021
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 1.1Jan 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

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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)53,8114
Polymers53,5962
Non-polymers2152
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-14 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.220, 86.591, 123.265
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 / 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-Q1Z / (3~{R})-3-methyl-2-oxidanylidene-pentanedioic acid


Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM Bis Tris Propane, 200 mM sodium/potassium phosphate, 20% w/v PEG 3350, 1 mM manganese chloride, 2 mM 3-methyl-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: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.53→86.59 Å / Num. obs: 48664 / % possible obs: 88.7 % / Redundancy: 11 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.6
Reflection shellResolution: 1.53→1.71 Å / Rmerge(I) obs: 1.289 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2433 / CC1/2: 0.665

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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: 1.53→50.21 Å / SU ML: 0.1407 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4488
RfactorNum. reflection% reflection
Rfree0.1922 2474 5.09 %
Rwork0.1624 --
obs0.1639 48587 59.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.61 Å2
Refinement stepCycle: LAST / Resolution: 1.53→50.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 0 474 4030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01173671
X-RAY DIFFRACTIONf_angle_d1.28064968
X-RAY DIFFRACTIONf_chiral_restr0.0593524
X-RAY DIFFRACTIONf_plane_restr0.0084648
X-RAY DIFFRACTIONf_dihedral_angle_d21.65051365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.774510.329925X-RAY DIFFRACTION0.59
1.56-1.60.349120.2829100X-RAY DIFFRACTION2.33
1.6-1.630.3156140.2883300X-RAY DIFFRACTION7.14
1.63-1.670.3758270.3071706X-RAY DIFFRACTION16.38
1.67-1.710.2609730.27841360X-RAY DIFFRACTION32.36
1.71-1.760.3033870.26731924X-RAY DIFFRACTION45.13
1.76-1.810.28961120.2612253X-RAY DIFFRACTION52.78
1.81-1.870.28881340.25112492X-RAY DIFFRACTION58.64
1.87-1.930.26381450.23162757X-RAY DIFFRACTION64.91
1.93-2.010.23371570.22793057X-RAY DIFFRACTION71.65
2.01-2.10.24442070.20613204X-RAY DIFFRACTION76.6
2.1-2.210.21041860.19523463X-RAY DIFFRACTION81.16
2.21-2.350.20772070.18853628X-RAY DIFFRACTION85.05
2.35-2.530.21442270.18063740X-RAY DIFFRACTION87.88
2.53-2.790.22891970.17344088X-RAY DIFFRACTION93.91
2.79-3.190.18962120.16324208X-RAY DIFFRACTION97.57
3.19-4.020.15842430.12724336X-RAY DIFFRACTION99.11
4.02-50.210.16082430.134472X-RAY DIFFRACTION97.96

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