6IWR | pdb_00006iwr

Crystal structure of GalNAc-T7 with UDP, GalNAc and Mn2+

PDB DOI: https://doi.org/10.2210/pdb6IWR/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2018-12-06 Released: 2019-02-06
Deposition Author(s): Yu, C., Yin, Y.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.220 (Depositor), 0.222 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of carbohydrate transfer activity of UDP-GalNAc: Polypeptide N-acetylgalactosaminyltransferase 7.

Yu, C., Liang, L., Yin, Y.

(2019) Biochem Biophys Res Commun 510: 266-271

PubMed: 30685086 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2019.01.084
Primary Citation Related Structures:
6IWQ, 6IWR

PubMed Abstract:
The UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferases (GalNAc-Ts) catalyze mucin-type O-glycosylation by transferring α-N-acetylgalactosamine (GalNAc) from UDP- GalNAc to Ser or Thr residues of target proteins. We resolved the crystal structures of GalNAc-T7, a GalNAc-T capable of glycosylating consecutive sites, and of its complex with the donor substrate UDP-GalNAc. The N-terminal catalytic domain and C-terminal lectin domain are connected by a flexible linker, forming a narrow cleft for the acceptor substrate. Only the α subdomain of the lectin domain binds to the glycosyl group, indicating that key residues determine substrate binding. Compared to the Apo structure, the loop covering the catalytic center of the complex show significant conformational changes, indicating the mechanism of the catalytic reaction.

Organizational Affiliation

Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.

Macromolecule Content

Total Structure Weight: 414.75 kDa
Atom Count: 27,072
Modeled Residue Count: 3,268
Deposited Residue Count: 3,582
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylgalactosaminyltransferase 7	A, B, C, D, E A, B, C, D, E, F	597	Homo sapiens	Mutation(s): 0 Gene Names: GALNT7 EC: 2.4.1 (PDB Primary Data), 2.4.1.41 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q86SF2 (Homo sapiens) Explore Q86SF2 Go to UniProtKB: Q86SF2
PHAROS: Q86SF2 GTEx: ENSG00000109586
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86SF2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD2 Query on UD2 Download:Ideal Coordinates CCD File SDF format, chain M [auth D] MOL2 format, chain M [auth D] mmCIF format, chain M [auth D]	M [auth D]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-NESSUJCYSA-N		Interactions Focus chain M [auth D] Interactions & Density Focus chain M [auth D]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] L [auth D] N [auth E] G [auth A], H [auth B], I [auth C], L [auth D], N [auth E], O [auth F]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain L [auth D] Focus chain N [auth E] Focus chain O [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.258 (Depositor), 0.258 (DCC)
R-Value Work: 0.220 (Depositor), 0.222 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.435	α = 90
b = 158.264	β = 90
c = 251.484	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-02-06

Deposition Author(s):

Yu, C.

Yin, Y.X.

Revision History (Full details and data files)

Version 1.0: 2019-02-06
Type: Initial release
Version 1.1: 2019-02-20
Changes: Data collection, Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary