6PXU

Crystal structure of human GalNAc-T12 bound to a diglycosylated peptide, Mn2+, and UDP

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Komagataella pastoris

  • Deposited: 2019-07-27 Released: 2019-09-25 
  • Deposition Author(s): Samara, N.L., Fernandez, A.J.
  • Funding Organization(s): National Institutes of Health/National Human Genome Research Institute; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.007 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function.

Fernandez, A.J.Daniel, E.J.P.Mahajan, S.P.Gray, J.J.Gerken, T.A.Tabak, L.A.Samara, N.L.

(2019) Proc.Natl.Acad.Sci.USA 116: 20404-20410

  • DOI: 10.1073/pnas.1902211116

  • PubMed Abstract: 
  • Polypeptide <i>N- </i>acetylgalactosaminyl transferases (GalNAc-Ts) initiate mucin type <i>O </i>-glycosylation by catalyzing the transfer of <i>N </i>-acetylgalactosamine (GalNAc) to Ser or Thr on a protein substrate. Inactive and partially activ ...

    Polypeptide N- acetylgalactosaminyl transferases (GalNAc-Ts) initiate mucin type O -glycosylation by catalyzing the transfer of N -acetylgalactosamine (GalNAc) to Ser or Thr on a protein substrate. Inactive and partially active variants of the isoenzyme GalNAc-T12 are present in subsets of patients with colorectal cancer, and several of these variants alter nonconserved residues with unknown functions. While previous biochemical studies have demonstrated that GalNAc-T12 selects for peptide and glycopeptide substrates through unique interactions with its catalytic and lectin domains, the molecular basis for this distinct substrate selectivity remains elusive. Here we examine the molecular basis of the activity and substrate selectivity of GalNAc-T12. The X-ray crystal structure of GalNAc-T12 in complex with a di-glycosylated peptide substrate reveals how a nonconserved GalNAc binding pocket in the GalNAc-T12 catalytic domain dictates its unique substrate selectivity. In addition, the structure provides insight into how colorectal cancer mutations disrupt the activity of GalNAc-T12 and illustrates how the rules dictating GalNAc-T12 function are distinct from those for other GalNAc-Ts.


    Organizational Affiliation

    Section on Biological Chemistry, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892.,Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218.,Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892 nadine.samara@nih.gov.,Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106.,Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, MD 21218.,Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polypeptide N-acetylgalactosaminyltransferase 12
A, B
543Homo sapiensMutation(s): 0 
Gene Names: GALNT12
EC: 2.4.1.41
Find proteins for Q8IXK2 (Homo sapiens)
Go to Gene View: GALNT12
Go to UniProtKB:  Q8IXK2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GAGATGAGAGYYITPRTGAGA
C, D
21N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
C, D
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.007 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.171 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 72.820α = 113.08
b = 73.123β = 100.50
c = 74.441γ = 108.23
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited States1 ZIA DE000739 05
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM113534

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-09
    Type: Data collection, Database references
  • Version 1.2: 2019-10-23
    Type: Data collection, Database references