5NQA | pdb_00005nqa

Crystal structure of GalNAc-T4 in complex with the monoglycopeptide 3

• PDB DOI: https://doi.org/10.2210/pdb5NQA/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2017-04-19 Released: 2017-12-20 
• Deposition Author(s): de las Rivas, M., Lira-Navarrete, E., Daniel, E.J.P., Companon, I., Coelho, H., Diniz, A., Jimenez-Barbero, J., Peregrina, J.M., Clausen, H., Corzana, F., Marcelo, F., Jimenez-Oses, G., Gerken, T.A., Hurtado-Guerrero, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

The interdomain flexible linker of the polypeptide GalNAc transferases dictates their long-range glycosylation preferences.

Rivas, M.L., Lira-Navarrete, E., Daniel, E.J.P., Companon, I., Coelho, H., Diniz, A., Jimenez-Barbero, J., Peregrina, J.M., Clausen, H., Corzana, F., Marcelo, F., Jimenez-Oses, G., Gerken, T.A., Hurtado-Guerrero, R.

(2017) Nat Commun 8: 1959-1959

• PubMed: 29208955 
• DOI: https://doi.org/10.1038/s41467-017-02006-0
• Primary Citation Related Structures: 
  5NQA


• PubMed Abstract: 
  

  The polypeptide GalNAc-transferases (GalNAc-Ts), that initiate mucin-type O-glycosylation, consist of a catalytic and a lectin domain connected by a flexible linker. In addition to recognizing polypeptide sequence, the GalNAc-Ts exhibit unique long-range N- and/or C-terminal prior glycosylation (GalNAc-O-Ser/Thr) preferences modulated by the lectin domain. Here we report studies on GalNAc-T4 that reveal the origins of its unique N-terminal long-range glycopeptide specificity, which is the opposite of GalNAc-T2. The GalNAc-T4 structure bound to a monoglycopeptide shows that the GalNAc-binding site of its lectin domain is rotated relative to the homologous GalNAc-T2 structure, explaining their different long-range preferences. Kinetics and molecular dynamics simulations on several GalNAc-T2 flexible linker constructs show altered remote prior glycosylation preferences, confirming that the flexible linker dictates the rotation of the lectin domain, thus modulating the GalNAc-Ts' long-range preferences. This work for the first time provides the structural basis for the different remote prior glycosylation preferences of the GalNAc-Ts.

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Organizational Affiliation: 
• BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain.
Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, DK-2200, Denmark.
Department of Biochemistry, Case Western Reserve University, Cleveland, 44106, OH, USA.
Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain.
UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade de Nova de Lisboa, Caparica, 2829-516, Portugal.
CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain.
Departament of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa, Bizkaia, 48940, Spain.
Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain.
Department of Pediatrics, Case Western Reserve University, Cleveland, 44106, OH, USA.
Department of Chemistry, Case Western Reserve University, Cleveland, 44106, OH, USA.
BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, 50018, Spain. [e-mail].
Fundación ARAID, 50018, Zaragoza, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 140.48 kDa 
• Atom Count: 10,430 
• Modeled Residue Count: 1,029 
• Deposited Residue Count: 1,172 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polypeptide N-acetylgalactosaminyltransferase 4	A, B	578	Homo sapiens	Mutation(s): 0  Gene Names: GALNT4 EC: 2.4.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4A0 (Homo sapiens) Explore Q8N4A0  Go to UniProtKB:  Q8N4A0
PHAROS:  Q8N4A0 GTEx:  ENSG00000257594

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoglycopeptide 3	C [auth G]	16	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGA	HC [auth G], UA [auth A]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N
GOL	DC [auth B], EC [auth B], FC [auth B], GC [auth B], OA [auth A], PA [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth A], AB [auth B], AC [auth B], BA [auth A], BB [auth B], BC [auth B], CA [auth A], CB [auth B], CC [auth B], D [auth A], DA [auth A], DB [auth B], E [auth A], EA [auth A], EB [auth B], F [auth A], FA [auth A], FB [auth B], G [auth A], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IA [auth A], IB [auth B], J [auth A], JA [auth A], JB [auth B], K [auth A], KA [auth A], KB [auth B], L [auth A], LA [auth A], LB [auth B], M [auth A], MA [auth A], MB [auth B], N [auth A], NA [auth A], NB [auth B], O [auth A], OB [auth B], P [auth A], PB [auth B], Q [auth A], QB [auth B], R [auth A], RB [auth B], S [auth A], SB [auth B], T [auth A], TB [auth B], U [auth A], UB [auth B], V [auth A], VA [auth B], VB [auth B], W [auth A], WA [auth B], WB [auth B], X [auth A], XA [auth B], XB [auth B], Y [auth A], YA [auth B], YB [auth B], Z [auth A], ZA [auth B], ZB [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.274 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.447	α = 116.47
b = 79.881	β = 96.74
c = 88.614	γ = 104.72

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): de las Rivas, M., Lira-Navarrete, E., Daniel, E.J.P., Companon, I., Coelho, H., Diniz, A., Jimenez-Barbero, J., Peregrina, J.M., Clausen, H., Corzana, F., Marcelo, F., Jimenez-Oses, G., Gerken, T.A., Hurtado-Guerrero, R.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-16
  Changes: Structure summary