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- PDB-8re5: Aspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in com... -

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Basic information

Entry
Database: PDB / ID: 8re5
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) R735Q variant in complex with Mn, 2-oxosuberate and a Factor X derived peptide fragment
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Coagulation factor X
KeywordsOXIDOREDUCTASE / AspH / Aspartyl/Asparaginyl beta-hydroxylase / 2-oxoglutarate / 2OG / alpha-ketoglutarate / substrate analogues
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 / positive regulation of calcium ion transport into cytosol / Protein hydroxylation / positive regulation of proteolysis / positive regulation of TOR signaling / detection of calcium ion / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / 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 / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Intrinsic Pathway of Fibrin Clot Formation / Ion homeostasis / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / phospholipid binding / regulation of protein stability / calcium ion transmembrane transport / Golgi lumen / 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 / external side of plasma membrane / serine-type endopeptidase activity / 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 / 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. / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
: / : / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBrasnett, A. / Hou, C. / Rabe, P. / Brewitz, L. / Schofield, C.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106244/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V001892/1 United Kingdom
Wellcome Trust227298/Z/23/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural and functional consequences of aspartate/asparagine-beta-hydroxylase variants causing Traboulsi Syndrome.
Authors: Hou, C.X. / Brasnett, A. / Rabe, P. / Schofield, C.J. / Brewitz, L.
History
DepositionDec 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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)55,8226
Polymers55,3552
Non-polymers4674
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-24 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.361, 86.343, 123.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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

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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: 51164.387 Da / Num. of mol.: 1 / Mutation: R735Q
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


Mass: 4190.384 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P00742

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Non-polymers , 4 types, 452 molecules

#3: Chemical ChemComp-YQX / 2-oxidanylideneoctanedioic acid


Mass: 188.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.43 Å3/Da / Density % sol: 49.41 % / Description: needle morphology, 300 um length
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M bis tris propane pH 7.5, 0.2 M NaBr, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→61.9 Å / Num. obs: 60246 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 17.7
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.9 % / Redundancy: 10 % / Rmerge(I) obs: 1.139 / Num. measured all: 29705 / Num. unique obs: 2967 / CC1/2: 0.713 / Rpim(I) all: 0.374 / Rrim(I) all: 1.201 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→61.9 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1990 3.31 %
Rwork0.1756 --
obs0.1767 60197 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→61.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 28 450 4026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153698
X-RAY DIFFRACTIONf_angle_d1.3145003
X-RAY DIFFRACTIONf_dihedral_angle_d6.411510
X-RAY DIFFRACTIONf_chiral_restr0.083526
X-RAY DIFFRACTIONf_plane_restr0.013657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.30061400.28744026X-RAY DIFFRACTION98
1.74-1.790.2521400.23534110X-RAY DIFFRACTION100
1.79-1.840.2171330.20554095X-RAY DIFFRACTION100
1.84-1.90.23311340.18994106X-RAY DIFFRACTION100
1.9-1.970.22721310.19784133X-RAY DIFFRACTION100
1.97-2.050.24141470.19984119X-RAY DIFFRACTION100
2.05-2.140.21211550.18514113X-RAY DIFFRACTION100
2.14-2.250.2651120.18864162X-RAY DIFFRACTION100
2.25-2.390.22181570.18594156X-RAY DIFFRACTION100
2.4-2.580.22471590.19134123X-RAY DIFFRACTION100
2.58-2.840.25581380.18694199X-RAY DIFFRACTION100
2.84-3.250.20171370.1824191X-RAY DIFFRACTION100
3.25-4.10.17871610.15124233X-RAY DIFFRACTION100
4.1-61.90.16811460.14834441X-RAY DIFFRACTION100

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