SASDBS2: Recombinant Tn antigen-binding lectin from Vatairea macrocarpa

Basic information

• Entry: Database: SASBDB / ID: SASDBS2

Sample

Recombinant Tn antigen-binding lectin from Vatairea macrocarpa

• Recombinant Tn antigen-binding lectin (protein), vRML, Vatairea macrocarpa

Function / homology

Function:

carbohydrate binding / metal ion binding

Domain/homology:

Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Concanavalin A-like lectin/glucanase domain superfamily

Component:

Seed lectin

• Biological species: Vatairea macrocarpa (plant)
• Citation: Journal: Int J Biochem Cell Biol / Year: 2016; Title: Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research.; Authors: Bruno L Sousa / José C Silva-Filho / Prashant Kumar / Melissa A Graewert / Ronniery I Pereira / Rodrigo M S Cunha / Kyria S Nascimento / Gustavo A Bezerra / Plínio Delatorre / Kristina Djinovic-Carugo / Celso S Nagano / Karl Gruber / Benildo S Cavada / ; Abstract: Legume lectins are the most thoroughly studied group of lectins and have been widely linked to many pathological processes. Their use as immunohistochemistry markers for cell profiling and cancer diagnosis have made these molecules important tools for immunological studies and have stimulated the prospection and characterization of new lectins. The crystal structures of a recombinant seed lectin from Vatairea macrocarpa (rVML) and its complexes with GalNAcα1-O-Ser, GalNAc and α-lactose, have been determined at 1.90, 1.97, 2.70 and 1.83Å resolution, respectively. Small angle X-ray scattering and calorimetry assays have confirmed the same pH stable oligomerization pattern and binding profiles proposed for its wild-type counterpart. In silico analyzes have explored the potential of this recombinant lectin as new tool for cancer research through a comparative profile with other legume lectins widely used for cancer diagnosis and prognosis. The results suggest the recognition of specific epitopes exhibited on different cancer cells as a process that relies on the disposition of hydrophobic clusters and charged regions around the lectin carbohydrate-binding site, favouring the anchorage of different groups in the antigen boundaries, highlighting the different potential of each analyzed lectin. In conclusion, the experimental results and comparative analysis show that rVML is as a promising tool for cancer research, able to bind with high affinity specific tumor-associated antigens, highly stable and easily produced.

Contact author

• Melissa Graewert (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #416: ; Type: atomic / Software: CORAL / Radius of dummy atoms: 1.90 A / Chi-square value: 0.920; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Recombinant Tn antigen-binding lectin from Vatairea macrocarpa; Specimen concentration: 1.00-10.00
• Buffer: Name: sodium phosphate / Concentration: 100.00 mM / pH: 5 / Composition: 150 mM NaCl, 5% v/v glycerol

Entity #273

Name: vRML / Type: protein / Description: Recombinant Tn antigen-binding lectin / Formula weight: 26.213 / Num. of mol.: 4 / Source: Vatairea macrocarpa / References: UniProt: P81371
Sequence:

SEVVSYSFTK FNPNPKDIIL QGDALVTSKG KLQLTKVKDG KPVDHSLGRA LYAAPIHIWD DSTDRVASFA TSFSFVVEAP DESKTADGIA FFLAPPDTQP QKDGGFLGLF NDSNKSIQTV AVEFDTFSNT WDPSARHIGI NVNSIESMKY VKWGWENGKV ANVYISYEAS TKTLTASLTY PSNATSYIVS ANVDLKSALP EWVRVGFSAT SGLSRDHVET HDVLDWSFTS TLQAPSDDSN

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Tn antigen-binding lectin from V. macrocarpa. / Measurement date: Jan 11, 2014 / Storage temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0199	4.4962

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 978 /

	Min	Max
Q	0.0778983	2.65196
P(R) point	1	978
R	0	9.5

Result

Type of curve: single_conc
Comments: Note: Carries a tyrosine mutation, instead of phenylalanine, at position 6 (F6Y - cf UniProt P81371).

	Experimental	Standard	Porod
MW	100 kDa	70 kDa	100 kDa
Volume	-	-	168 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	1787	1.8	1813.1	2.8
Radius of gyration, Rg	3.13 nm	0.02	3.17 nm	0.4

	Min	Max
D	-	9.5
Guinier point	23	148