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- PDB-6tex: Crystal Structure of full-length Human Lysyl Hydroxylase LH3 - Va... -

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Basic information

Entry
Database: PDB / ID: 6tex
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucose
ComponentsMultifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
KeywordsTRANSFERASE / Collagen / lysyl hydroxylase / hydroxylysine / galactosyltransferase / glucosyltransferase
Function / homology
Function and homology information


procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen galactosyltransferase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / basement membrane assembly / epidermis morphogenesis ...procollagen glucosyltransferase / peptidyl-lysine hydroxylation / procollagen glucosyltransferase activity / hydroxylysine biosynthetic process / procollagen-lysine 5-dioxygenase / procollagen galactosyltransferase / procollagen-lysine 5-dioxygenase activity / procollagen galactosyltransferase activity / basement membrane assembly / epidermis morphogenesis / Collagen biosynthesis and modifying enzymes / collagen metabolic process / endothelial cell morphogenesis / protein O-linked glycosylation / collagen fibril organization / L-ascorbic acid binding / neural tube development / small molecule binding / lung morphogenesis / rough endoplasmic reticulum / trans-Golgi network / vasodilation / intracellular protein localization / : / in utero embryonic development / iron ion binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / 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. / q2cbj1_9rhob like domain / 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. ...Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / : / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / : / URIDINE-5'-DIPHOSPHATE / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChiapparino, A. / De Giorgi, F. / Scietti, L. / Faravelli, S. / Roscioli, T. / Forneris, F.
Funding support Italy, 4items
OrganizationGrant numberCountry
European CommissionMSCA-IF 745934 - COTETHERS
Italian Association for Cancer Research20075 Italy
Other privateThe Giovanni Armenise-Harvard Foundation CDA 2013 Italy
Italian Ministry of EducationDipartimenti di Eccellenza Program 2018-2022 Italy
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
DepositionNov 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author / database_2
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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,36110
Polymers82,8141
Non-polymers1,5479
Water1,982110
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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)168,72220
Polymers165,6292
Non-polymers3,09318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Unit cell
Length a, b, c (Å)98.049, 100.409, 225.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

21A-1009-

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: 82814.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Val80Lys Mutation - First Ser residue and last three Ala residues were introduced by molecular cloning
Source: (gene. exp.) Homo sapiens (human) / Gene: PLOD3 / Cell line (production host): HEK293F / 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 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: isolated from a genetically manipulated source
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, 117 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.35 Å3/Da / Density % sol: 63.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 600 mM sodium formate, 12% PGA-LM, 100 mM HEPES/NaOH, 500 uM FeCl2, 500 uM MnCl2, 1 mM UDP-Glucose
Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.02 Å / Num. obs: 49068 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 38.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.071 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 1.351 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4243 / CC1/2: 0.461 / Rpim(I) all: 1.155

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FXK

6fxk


Resolution: 2.3→49 Å / SU ML: 0.3122 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.529
RfactorNum. reflection% reflection
Rfree0.2261 1609 4.78 %
Rwork0.1696 --
obs0.1723 33658 67.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 92 110 5919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085992
X-RAY DIFFRACTIONf_angle_d0.96568142
X-RAY DIFFRACTIONf_chiral_restr0.0532849
X-RAY DIFFRACTIONf_plane_restr0.00621062
X-RAY DIFFRACTIONf_dihedral_angle_d14.45463524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.3552330.2342847X-RAY DIFFRACTION19.79
2.37-2.460.2825580.24561293X-RAY DIFFRACTION30.12
2.46-2.560.3233900.24271568X-RAY DIFFRACTION37.17
2.56-2.670.31891010.26881977X-RAY DIFFRACTION46.53
2.67-2.820.34331290.24922402X-RAY DIFFRACTION56.07
2.82-2.990.31111260.22142892X-RAY DIFFRACTION67.59
2.99-3.220.2751830.20893637X-RAY DIFFRACTION85.12
3.22-3.550.21571800.18274323X-RAY DIFFRACTION99.47
3.55-4.060.19862200.15054318X-RAY DIFFRACTION99.98
4.06-5.110.18752560.12534311X-RAY DIFFRACTION99.8
5.11-490.21542330.15464481X-RAY DIFFRACTION99.6
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)
11.171812838990.1839564592280.2050947232142.06882526737-0.03373169014832.822247544990.0392792939650.188567248832-0.0788750058482-0.31330864592-0.03686674848670.142472554632-0.219852335734-0.259492800616-0.02235993120360.2036173960050.0748974340648-0.03401836817380.280180553045-0.0451400758720.27944123328761.498176838225.3231212006147.913782021
21.085134169640.347987733360.8840728169881.517094146230.1307520845970.6947443659910.153115548089-0.00319934127149-0.1122597379790.07503052803120.0605202108196-0.392445198816-0.005287798742060.341238427921-0.1275413945120.258788446718-0.0460351833854-0.08175217630370.2772680365250.010061258730.33143938369579.42866901133.8354006667183.722341249
31.408667760480.1553130727940.2384166008352.827597420910.5018305591922.797040558760.09199373306-0.06855064534630.04376996001210.279493348988-0.0411062172863-0.07700319599690.0973497008474-0.0240035824686-0.06189347201350.166318543975-0.0341153885129-0.02801407289620.1865795646570.041129257270.28045342178172.739856645835.0307707211182.911659125
40.7585206520210.2204282310370.589184654310.525291968525-0.1621284417433.321150603760.079170326276-0.0709539439557-0.01297686531910.1983571529710.06420343650270.1111403413010.0732866354195-0.386304200431-0.104983137060.256643224846-0.0310951230568-0.003560393822940.2657837214410.05606997014520.34657794952866.803896114834.4913694528183.18849457
51.18305516766-0.4050764052120.4385523956432.61927548916-0.376814118152.169144640770.0187801369945-0.1231498964180.01948281782360.261995210427-0.0974465890486-0.035233312915-0.1221251572060.1630792078170.05757685548210.375178300594-0.0855614970185-0.03199334901610.3578060593790.07760545833930.219582537979.135216513617.4962791686220.81920633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 267 )
2X-RAY DIFFRACTION2chain 'A' and (resid 268 through 336 )
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 474 )
4X-RAY DIFFRACTION4chain 'A' and (resid 475 through 527 )
5X-RAY DIFFRACTION5chain 'A' and (resid 528 through 738 )

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