5AJP

Crystal structure of the active form of GalNAc-T2 in complex with UDP and the glycopeptide MUC5AC-13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Dynamic Interplay between Catalytic and Lectin Domains of Galnac-Transferases Modulates Protein O-Glycosylation.

Lira-Navarrete, E.De Las Rivas, M.Companon, I.Pallares, M.C.Kong, Y.Iglesias-Fernandez, J.Bernardes, G.J.L.Peregrina, J.M.Rovira, C.Bernado, P.Bruscolini, P.Clausen, H.Lostao, A.Corzana, F.Hurtado-Guerrero, R.

(2015) Nat Commun 6: 6937

  • DOI: 10.1038/ncomms7937
  • Primary Citation of Related Structures:  
    5AJO, 5AJN, 5AJP

  • PubMed Abstract: 
  • Protein O-glycosylation is controlled by polypeptide GalNAc-transferases (GalNAc-Ts) that uniquely feature both a catalytic and lectin domain. The underlying molecular basis of how the lectin domains of GalNAc-Ts contribute to glycopeptide specificity and catalysis remains unclear ...

    Protein O-glycosylation is controlled by polypeptide GalNAc-transferases (GalNAc-Ts) that uniquely feature both a catalytic and lectin domain. The underlying molecular basis of how the lectin domains of GalNAc-Ts contribute to glycopeptide specificity and catalysis remains unclear. Here we present the first crystal structures of complexes of GalNAc-T2 with glycopeptides that together with enhanced sampling molecular dynamics simulations demonstrate a cooperative mechanism by which the lectin domain enables free acceptor sites binding of glycopeptides into the catalytic domain. Atomic force microscopy and small-angle X-ray scattering experiments further reveal a dynamic conformational landscape of GalNAc-T2 and a prominent role of compact structures that are both required for efficient catalysis. Our model indicates that the activity profile of GalNAc-T2 is dictated by conformational heterogeneity and relies on a flexible linker located between the catalytic and the lectin domains. Our results also shed light on how GalNAc-Ts generate dense decoration of proteins with O-glycans.


    Organizational Affiliation

    1] BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain [2] Fundación ARAID, 50018 Zaragoza, Spain.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2A571Homo sapiensMutation(s): 1 
Gene Names: GALNT2
EC: 2.4.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for Q10471 (Homo sapiens)
Explore Q10471 
Go to UniProtKB:  Q10471
PHAROS:  Q10471
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MUCINB17Homo sapiensMutation(s): 0 
Gene Names: MUC5ACMUC5
UniProt & NIH Common Fund Data Resources
Find proteins for P98088 (Homo sapiens)
Explore P98088 
Go to UniProtKB:  P98088
PHAROS:  P98088
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
C [auth A]URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
A2G
Query on A2G

Download Ideal Coordinates CCD File 
Z [auth B]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
D [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [auth A],  V [auth A],  W [auth A],  X [auth A],  Y [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.266α = 90
b = 87.266β = 90
c = 178.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-05-20
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary