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- PDB-9fvy: Aspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, ... -

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Basic information

Entry
Database: PDB / ID: 9fvy
TitleAspartyl/Asparaginyl beta-hydroxylase (AspH) in complex with Fe, 2-oxoglutarate, succinate and the hudroxylated product of Factor X derived peptide fragment after O2 exposure
Components
  • Aspartyl/asparaginyl beta-hydroxylase
  • Factor X light chain
KeywordsOXIDOREDUCTASE / AspH / Aspartyl/Asparaginyl beta-hydroxylase / O2 exposure / product complex
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 / cortical endoplasmic reticulum / limb morphogenesis ...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 / cortical endoplasmic reticulum / limb morphogenesis / 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 / : / face morphogenesis / structural constituent of muscle / response to ATP / positive regulation of proteolysis / roof of mouth development / Protein hydroxylation / positive regulation of calcium ion transport into cytosol / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / : / Gamma-carboxylation of protein precursors / detection of calcium ion / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / calcium ion homeostasis / : / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to calcium ion / muscle contraction / regulation of protein stability / phospholipid binding / Golgi lumen / Stimuli-sensing channels / calcium ion transmembrane transport / 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 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
2-OXOGLUTARIC ACID / : / DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / Coagulation factor X / Aspartyl/asparaginyl beta-hydroxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrasnett, A. / de Munnik, M. / Brewitz, L. / Rabe, P. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003291/1 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of the promiscuity of the unusual Fe(II) and 2-oxoglutarate dependent human aspartate/asparagine-beta-hydroxylase.
Authors: de Munnik, M. / Brasnett, A. / Zhou, T. / Myers, W. / Wang, Y. / Chatterjee, K. / Tumber, A. / Marshall, S.A. / Simon, P.S. / Aller, P. / Shilova, A. / Axford, D. / Makita, H. / Paley, D.W. ...Authors: de Munnik, M. / Brasnett, A. / Zhou, T. / Myers, W. / Wang, Y. / Chatterjee, K. / Tumber, A. / Marshall, S.A. / Simon, P.S. / Aller, P. / Shilova, A. / Axford, D. / Makita, H. / Paley, D.W. / Tiwari, V. / Stead, A.T. / Dehe, S. / Sanchez, H. / Rosenberg, D.J. / Alonso-Mori, R. / Bhowmick, A. / Yano, J. / Yachandra, V.K. / Park, J. / Park, S. / Orville, A.M. / Brewitz, L. / Kern, J.F. / Schofield, C.J. / Rabe, P.
History
DepositionJun 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartyl/asparaginyl beta-hydroxylase
B: Factor X light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2729
Polymers53,6122
Non-polymers6607
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-23 kcal/mol
Surface area19400 Å2
Unit cell
Length a, b, c (Å)50.260, 86.830, 123.330
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

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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
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 Factor X light chain


Mass: 4206.383 Da / Num. of mol.: 1 / Mutation: C90S, C95S, C112S, C121S / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P00742

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Non-polymers , 7 types, 338 molecules

#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.51 Å3/Da / Density % sol: 50.99 % / Description: needle morphology, 4 um x 4 um x 300 um
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting 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: Aug 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→50.28 Å / Num. obs: 43435 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 33.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.029 / Rrim(I) all: 0.106 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.924 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2165 / CC1/2: 0.656 / Rpim(I) all: 0.541 / Rrim(I) all: 1.999 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.5 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 2000 4.61 %
Rwork0.1778 41363 -
obs0.1788 43363 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 38 331 3915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363705
X-RAY DIFFRACTIONf_angle_d0.61065006
X-RAY DIFFRACTIONf_chiral_restr0.043527
X-RAY DIFFRACTIONf_plane_restr0.0054654
X-RAY DIFFRACTIONf_dihedral_angle_d12.961386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30051410.28662915X-RAY DIFFRACTION99.93
1.95-20.25331400.23842887X-RAY DIFFRACTION100
2-2.060.26121410.21452922X-RAY DIFFRACTION100
2.06-2.130.2551410.21112920X-RAY DIFFRACTION100
2.13-2.20.25641410.20012920X-RAY DIFFRACTION100
2.2-2.290.24181430.18912947X-RAY DIFFRACTION99.97
2.29-2.390.2241400.17982908X-RAY DIFFRACTION100
2.39-2.520.22061420.1832939X-RAY DIFFRACTION100
2.52-2.680.21231420.18652912X-RAY DIFFRACTION100
2.68-2.880.20551420.20242967X-RAY DIFFRACTION99.97
2.88-3.170.27461440.20422963X-RAY DIFFRACTION100
3.17-3.630.20331440.18212979X-RAY DIFFRACTION100
3.63-4.580.14921470.14033042X-RAY DIFFRACTION100
4.58-43.50.15321520.15583142X-RAY DIFFRACTION99.94
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)
12.68672885451-0.592312986220.8979159779832.04587575131-0.7364924407636.008295168740.2103550911320.2575721239970.11909721565-0.302755083953-0.153792127072-0.3655369161090.1358367590970.489593714195-0.06800635126730.3178493653740.04495607216420.08354091203360.2466732812530.0002196458676330.381239336441-6.83287627725-4.86504689488-0.357646466969
20.5547162239370.262686768198-0.9692149416962.33361860847-2.379741715413.493710238610.1384137001640.0400017817861-0.00456922872737-0.03385988322350.1792981682420.2028528791720.112982258414-0.356483674955-0.3127830704280.332682576079-0.109914061182-0.05781602532160.4068638772060.02189505414690.299248324476-22.3046834433-19.333562704919.7437858463
31.760466910780.2776449941370.6495205132181.017019860030.08830294707662.145833662320.000120568556010.254676074045-0.0805503277019-0.1751559170690.04778378335140.03693435888970.1205724615330.0953405855814-0.0480646064030.2373669418520.011532942319-0.004653267768390.2457020889110.0006517388052240.261279688377-4.02432085631-25.81588709345.4430747709
47.09183807914-2.043897679351.540218322927.03797408511-2.310331625132.00080930264-0.1270828344260.3178959054210.499821975665-0.0811322794801-0.351685605960.448001361134-0.550855989226-0.5622792364960.4751966079380.4283253191670.0195374709124-0.06661578402470.51032700159-0.02157946675160.449259907261-10.6374504399-20.020993700438.5163716877
58.19047681516-2.186408527031.682638269386.81446757253-2.962938659388.776747409120.2245065982740.0515132363739-0.02944307049980.03875380554870.1881058602680.09146599774780.329180829786-0.274339195192-0.4118438640390.37360783499-0.0424654716866-0.05371601300670.544595679175-0.003522845948190.321996311867-14.4622821771-20.916531659330.1889432853
61.432513564212.76778463843-3.751008223025.43219558134-7.319425983299.89687983637-0.2098789077760.0943435324710.4040096870390.11552370349-0.0883110424472-0.135674448327-0.3631669226430.220957545570.3188431552070.517970379051-0.129424789583-0.1014191789980.6212901253760.07642460425520.462595227655-5.08037012612-12.908857292924.763379343
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 330 through 410 )AA330 - 4101 - 81
22chain 'A' and (resid 411 through 537 )AA411 - 53782 - 208
33chain 'A' and (resid 538 through 758 )AA538 - 758209 - 429
44chain 'B' and (resid 99 through 104 )BH99 - 1041 - 6
55chain 'B' and (resid 105 through 109 )BH105 - 1097 - 11
66chain 'B' and (resid 110 through 116 )BH110 - 11612 - 18

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