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

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Basic information

Entry
Database: PDB / ID: 6tez
TitleCrystal Structure of full-length Human Lysyl Hydroxylase LH3 - Val80Lys mutant - Cocrystal with Fe2+, Mn2+, UDP-Glucuronic Acid
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 / PLOD GT domain / 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 ...Procollagen-lysine 5-dioxygenase, conserved site / PLOD GT domain / 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-GLUCURONIC ACID / Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 6, 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)84,53710
Polymers82,8141
Non-polymers1,7239
Water1,31573
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)169,07520
Polymers165,6292
Non-polymers3,44618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area6790 Å2
ΔGint-60 kcal/mol
Surface area58370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.001, 99.770, 224.461
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-906-

HOH

21A-949-

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, 80 molecules

#3: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O18P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#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.: 73 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
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-Glucuronic Acid
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: 2.7→49 Å / Num. obs: 30477 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 41.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.088 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.83 Å / Rmerge(I) obs: 1.312 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3911 / CC1/2: 0.58 / Rpim(I) all: 0.902

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Processing

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

6fxk


Resolution: 2.7→49 Å / SU ML: 0.3007 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2911
RfactorNum. reflection% reflection
Rfree0.2278 1339 5.12 %
Rwork0.1895 --
obs0.1915 26155 85.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.73 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5692 0 104 73 5869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285985
X-RAY DIFFRACTIONf_angle_d0.63138136
X-RAY DIFFRACTIONf_chiral_restr0.0452852
X-RAY DIFFRACTIONf_plane_restr0.00441059
X-RAY DIFFRACTIONf_dihedral_angle_d17.58023515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.3296720.28581388X-RAY DIFFRACTION48.15
2.8-2.910.2824650.26451729X-RAY DIFFRACTION59.68
2.91-3.040.29991020.26192012X-RAY DIFFRACTION69.7
3.04-3.20.27391170.25772333X-RAY DIFFRACTION81.67
3.2-3.40.31711490.22222723X-RAY DIFFRACTION95.04
3.4-3.660.22161630.19512893X-RAY DIFFRACTION99.45
3.66-4.030.22461660.17462871X-RAY DIFFRACTION99.67
4.03-4.620.21821800.14382891X-RAY DIFFRACTION99.87
4.62-5.810.16061520.15732949X-RAY DIFFRACTION99.81
5.81-490.20271730.18063027X-RAY DIFFRACTION99.5
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)
11.061563941460.2498803740960.2903233260591.307828060490.6712002920253.35776599687-0.02057296674420.2520379415580.0200917045424-0.36768913046-0.0730914172470.0353850836622-0.531457135235-0.4195456665610.03952596536160.2541389635730.131499761509-0.01966036872070.299518237595-0.03785186269280.27035175093361.134346648625.622501645145.989346297
20.8728934458030.1913118956860.2901950729680.4602481963260.1976099077151.564244414610.070903829441-0.0567917961956-0.02230680445420.214753590762-0.0554696651231-0.1113358499570.06150762799140.0037754954705-0.01839025496580.175955532439-0.0141817719724-0.01057083743510.1814235703910.02193916070790.25964496061972.045845283232.9243074196181.543960791
30.968797393314-0.3134291713930.5632525022212.50652958295-0.4810117150911.79496629149-0.0343543072108-0.1309590952310.02485858598090.283395433746-0.0404250978499-0.0189357829477-0.1097006956780.1944839484390.05229004797710.439059898272-0.0609814423353-0.01209730488230.3392347130190.04445044617840.22564198384279.905641721217.0472490292220.88770574
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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