SASDDW4: Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS

Basic information

• Entry: Database: SASBDB / ID: SASDDW4

Sample

Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS

• Procollagen lysyl hydroxylase LH3 (protein), LH3, Homo sapiens

Function / homology

Function:

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

Domain/homology:

Procollagen-lysine 5-dioxygenase, conserved site / Lysyl hydroxylase signature. / PLOD GT domain / : / 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

Component:

Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3

• Biological species: Homo sapiens (human)
• Citation: Journal: Nat Commun / Year: 2018; Title: Molecular architecture of the multifunctional collagen lysyl hydroxylase and glycosyltransferase LH3.; Authors: Luigi Scietti / Antonella Chiapparino / Francesca De Giorgi / Marco Fumagalli / Lela Khoriauli / Solomon Nergadze / Shibom Basu / Vincent Olieric / Lucia Cucca / Blerida Banushi / Antonella Profumo / Elena Giulotto / Paul Gissen / Federico Forneris / ; Abstract: Lysyl hydroxylases catalyze hydroxylation of collagen lysines, and sustain essential roles in extracellular matrix (ECM) maturation and remodeling. Malfunctions in these enzymes cause severe connective tissue disorders. Human lysyl hydroxylase 3 (LH3/PLOD3) bears multiple enzymatic activities, as it catalyzes collagen lysine hydroxylation and also their subsequent glycosylation. Our understanding of LH3 functions is currently hampered by lack of molecular structure information. Here, we present high resolution crystal structures of full-length human LH3 in complex with cofactors and donor substrates. The elongated homodimeric LH3 architecture shows two distinct catalytic sites at the N- and C-terminal boundaries of each monomer, separated by an accessory domain. The glycosyltransferase domain displays distinguishing features compared to other known glycosyltransferases. Known disease-related mutations map in close proximity to the catalytic sites. Collectively, our results provide a structural framework characterizing the multiple functions of LH3, and the molecular mechanisms of collagen-related diseases involving human lysyl hydroxylases.

Contact author

• Federico Forneris (University of Pavia)

Models

• Model #1862: ; Type: dummy / Radius of dummy atoms: 1.90 A / Chi-square value: 1.85; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS; Specimen concentration: 3.5 mg/ml
• Buffer: Name: 25 mM HEPES, 200 mM NaCl / pH: 8

Entity #1000

Name: LH3 / Type: protein / Description: Procollagen lysyl hydroxylase LH3 / Formula weight: 90 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: O60568
Sequence:

SSDRPRGRDP VNPEKLLVIT VATAETEGYL RFLRSAEFFN YTVRTLGLGE EWRGGDVART VGGGQKVRWL KKEMEKYADR EDMIIMFVDS YDVILAGSPT ELLKKFVQSG SRLLFSAESF CWPEWGLAEQ YPEVGTGKRF LNSGGFIGFA TTIHQIVRQW KYKDDDDDQL FYTRLYLDPG LREKLSLNLD HKSRIFQNLN GALDEVVLKF DRNRVRIRNV AYDTLPIVVH GNGPTKLQLN YLGNYVPNGW TPEGGCGFCN QDRRTLPGGQ PPPRVFLAVF VEQPTPFLPR FLQRLLLLDY PPDRVTLFLH NNEVFHEPHI ADSWPQLQDH FSAVKLVGPE EALSPGEARD MAMDLCRQDP ECEFYFSLDA DAVLTNLQTL RILIEENRKV IAPMLSRHGK LWSNFWGALS PDEYYARSED YVELVQRKRV GVWNVPYISQ AYVIRGDTLR MELPQRDVFS GSDTDPDMAF CKSFRDKGIF LHLSNQHEFG RLLATSRYDT EHLHPDLWQI FDNPVDWKEQ YIHENYSRAL EGEGIVEQPC PDVYWFPLLS EQMCDELVAE MEHYGQWSGG RHEDSRLAGG YENVPTVDIH MKQVGYEDQW LQLLRTYVGP MTESLFPGYH TKARAVMNFV VRYRPDEQPS LRPHHDSSTF TLNVALNHKG LDYEGGGCRF LRYDCVISSP RKGWALLHPG RLTHYHEGLP TTWGTRYIMV SFVDPAAA

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.09919 Å / Dist. spec. to detc.: 2.87 mm
• Detector: Name: Pilatus 1M / Pixsize x: 172 mm

Scan

Title: Procollagen lysyl hydroxylase LH3 measured using SEC-SAXS
Measurement date: Feb 28, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 75 / Unit: 1/nm /

	Min	Max
Q	0.0513	4.9277

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 319 /

	Min	Max
Q	0.0888823	1.58136
P(R) point	1	319
R	0	20.96

Result

Type of curve: sec
Comments: The sample was injected at a load concentration of 3.5 mg/mL. The SEC column used was a Superdex 200 PC 3.2/300 Increase (GE Healthcare) at a flow rate 0.075 mL/min.

	Experimental	Standard	Standard error	Porod
MW	180 kDa	184 kDa	6	170 kDa
Volume	-	-	-	268 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	62.4	0.1	61.5	0.12
Radius of gyration, Rg	5.346 nm	0.02	5.05 nm	0.07

	Min	Max
D	-	20.96
Guinier point	9	43