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

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Basic information

Entry
Database: PDB / ID: 6teu
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+
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 / : / : / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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

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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)83,9579
Polymers82,8141
Non-polymers1,1438
Water00
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)167,91418
Polymers165,6292
Non-polymers2,28516
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Unit cell
Length a, b, c (Å)98.004, 100.691, 225.674
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

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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 / Mutation: V80K
Source method: isolated from a genetically manipulated source
Details: Val80Lys mutant - 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
#7: 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 , 4 types, 6 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: 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

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Details

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: 3.36 Å3/Da / Density % sol: 63.41 %
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
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 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.14 Å / Num. obs: 22529 / % possible obs: 98.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 47.02 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.186 / Net I/σ(I): 4.5
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 3.045 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3578 / CC1/2: 0.49 / Rpim(I) all: 2.479

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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: 3→49.14 Å / SU ML: 0.3595 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.0203
RfactorNum. reflection% reflection
Rfree0.2412 695 4.63 %
Rwork0.2079 --
obs0.2096 15011 65.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.33 Å2
Refinement stepCycle: LAST / Resolution: 3→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 67 0 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335895
X-RAY DIFFRACTIONf_angle_d0.58548009
X-RAY DIFFRACTIONf_chiral_restr0.0438838
X-RAY DIFFRACTIONf_plane_restr0.0051048
X-RAY DIFFRACTIONf_dihedral_angle_d15.19743487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.3804400.2951950X-RAY DIFFRACTION22.14
3.23-3.560.2829630.24861535X-RAY DIFFRACTION35.5
3.56-4.070.27791500.22763043X-RAY DIFFRACTION70.77
4.07-5.130.22342170.18774330X-RAY DIFFRACTION99.47
5.13-49.140.22212250.19984458X-RAY DIFFRACTION99.51
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)
10.6104883950430.07012818130090.1498073664330.623573823360.07671684194050.807510607328-0.02228645646760.126354754801-0.0933348163201-0.151211364484-0.132822498963-0.0230527549275-0.181015045079-0.188767204909-0.09257061177510.117205603640.0676917680611-0.02322186717420.169915908144-0.04734865768090.14499451769261.524861710125.3136074298146.244530909
20.4053074563880.180013758640.158566813420.5320146654980.4344913003820.6862588079270.02321488376380.05837857801010.04358362374570.1363211357710.0152731588469-0.07416147896960.0152760750321-0.0434585575650.02648067462020.109984717469-0.0353390871266-0.07576499457720.04421926482230.01267651507610.18767723683972.158976187433.4884194598182.475722746
30.545980533114-0.2844650300280.2185495383470.8679246853970.1773379841540.523650648458-0.0559635133991-0.04557300451510.0189190288080.0655441529875-0.01669313303540.0851866288952-0.02605140298590.125548832003-0.00116632323810.219647288994-0.0552895008508-0.05243263921030.1962061262630.02766988304050.064369536325579.287284309617.2292663231222.009924942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 242 )
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 536 )
3X-RAY DIFFRACTION3chain 'A' and (resid 537 through 738 )

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