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- PDB-8one: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - As... -

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Basic information

Entry
Database: PDB / ID: 8one
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Asp190Ser mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose
ComponentsMultifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
KeywordsTRANSFERASE / Collagen biosynthesis / extracellular matrix / post-translational modifications / collagen glycosylations / glycosyltransferase / lysyl hydroxylase
Function / homology
Function and homology information


procollagen galactosyltransferase / procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen galactosyltransferase activity / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / basement membrane assembly / epidermis morphogenesis ...procollagen galactosyltransferase / procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen galactosyltransferase activity / procollagen-lysine 5-dioxygenase / procollagen-lysine 5-dioxygenase activity / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / L-ascorbic acid binding / collagen fibril organization / neural tube development / lung morphogenesis / small molecule binding / rough endoplasmic reticulum / trans-Golgi network / vasodilation / protein localization / collagen-containing extracellular matrix / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMattoteia, D. / De Marco, M. / Pinnola, A. / Faravelli, S. / Scietti, L. / Forneris, F.
Funding support United States, Italy, Japan, 4items
OrganizationGrant numberCountry
The Giovanni Armenise-Harvard FoundationCDA 2013 United States
Italian Association for Cancer ResearchMFAG 20075 Italy
Italian Association for Cancer ResearchBridge 27004 Italy
Mizutani Foundation for Glycoscience200039 Japan
CitationJournal: Int J Mol Sci / Year: 2023
Title: Identification of Regulatory Molecular "Hot Spots" for LH/PLOD Collagen Glycosyltransferase Activity.
Authors: Mattoteia, D. / Chiapparino, A. / Fumagalli, M. / De Marco, M. / De Giorgi, F. / Negro, L. / Pinnola, A. / Faravelli, S. / Roscioli, T. / Scietti, L. / Forneris, F.
History
DepositionApr 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 9, 2023Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] ..._pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[3]
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,61411
Polymers82,8131
Non-polymers1,80110
Water5,819323
1
A: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
hetero molecules

A: Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,22922
Polymers165,6272
Non-polymers3,60220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)97.090, 100.181, 223.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1262-

HOH

21A-1310-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3


Mass: 82813.453 Da / Num. of mol.: 1 / Mutation: Asp190Ser
Source method: isolated from a genetically manipulated source
Details: Sequence GS at the N-terminus and AAA at C-terminus are cloning scars.,Sequence GS at the N-terminus and AAA at C-terminus are cloning scars.
Source: (gene. exp.) Homo sapiens (human) / Gene: PLOD3 / Plasmid: pUPE.106.08 / Cell (production host): HEK293-F / Production host: Homo sapiens (human)
References: UniProt: O60568, procollagen-lysine 5-dioxygenase, procollagen galactosyltransferase, procollagen glucosyltransferase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 331 molecules

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


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 600 mM sodium formate, 12% poly-glutamic-acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.775 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.775 Å / Relative weight: 1
ReflectionResolution: 2.3→48.88 Å / Num. obs: 48804 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.107 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.827 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4443 / CC1/2: 0.587 / Rpim(I) all: 1.255 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.44 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1903 5.02 %
Rwork0.204 --
obs0.2052 37883 77.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5713 0 73 323 6109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025963
X-RAY DIFFRACTIONf_angle_d0.4778102
X-RAY DIFFRACTIONf_dihedral_angle_d12.612194
X-RAY DIFFRACTIONf_chiral_restr0.042851
X-RAY DIFFRACTIONf_plane_restr0.0041050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3119700.29941385X-RAY DIFFRACTION42
2.36-2.420.2916690.27611512X-RAY DIFFRACTION46
2.42-2.490.2847890.27471673X-RAY DIFFRACTION51
2.49-2.570.32961380.27331896X-RAY DIFFRACTION59
2.57-2.660.31711240.26962129X-RAY DIFFRACTION65
2.67-2.770.30921330.26892298X-RAY DIFFRACTION70
2.77-2.90.29231450.26092554X-RAY DIFFRACTION78
2.9-3.050.2721290.2562790X-RAY DIFFRACTION84
3.05-3.240.29121610.24352980X-RAY DIFFRACTION91
3.24-3.490.23821700.2023267X-RAY DIFFRACTION98
3.49-3.840.20591540.18543323X-RAY DIFFRACTION100
3.84-4.40.17361790.15813338X-RAY DIFFRACTION100
4.4-5.540.16721810.15573351X-RAY DIFFRACTION100
5.54-47.440.19731610.18783484X-RAY DIFFRACTION99
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)
10.89060.90850.53931.46150.57762.388-0.08560.25640.0845-0.29550.0139-0.031-0.5703-0.04280.0260.23680.03240.04270.22390.00570.194319.105431.6599-77.7894
20.89750.7485-0.60021.84161.21392.5812-0.05580.1294-0.0976-0.4693-0.09730.11970.0392-0.8419-0.1241-0.01540.0923-0.06980.3176-0.11240.18919.144621.376-75.1175
31.6701-0.1550.09551.0935-0.74660.8030.26510.07790.00930.1767-0.2006-0.2899-0.2548-0.04210.13470.2132-0.1578-0.14110.20110.02610.287130.811237.3506-37.7151
41.10940.51270.00042.2103-0.00922.5620.0595-0.07240.08060.2958-0.0692-0.19970.01-0.0117-0.02520.0938-0.0615-0.05890.11950.02330.229223.682434.9485-41.8313
50.68310.21550.47090.2435-0.39481.71950.0927-0.08280.01860.1959-0.03720.07060.1244-0.1949-0.09130.2214-0.04140.00710.17340.03680.234818.066733.2576-38.1582
61.0392-0.15290.14742.2652-0.36821.5815-0.0938-0.08560.03460.06810.0039-0.0457-0.08210.21430.09590.2633-0.0714-0.03470.29270.05320.169230.921117.2143-3.8503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 277 )
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 336 )
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 474 )
5X-RAY DIFFRACTION5chain 'A' and (resid 475 through 536 )
6X-RAY DIFFRACTION6chain 'A' and (resid 537 through 738 )

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