8V9Q | pdb_00008v9q

Crystal structure of mGalNAc-T1 in complex with the mucin glycopeptide Muc5AC-13, Mn2+, and UDP.

PDB DOI: https://doi.org/10.2210/pdb8V9Q/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus, Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2023-12-08 Released: 2024-03-13
Deposition Author(s): Samara, N.L., Collette, A.M.
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.278 (Depositor), 0.285 (DCC)
R-Value Work:
0.248 (Depositor), 0.260 (DCC)
R-Value Observed:
0.249 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

An unusual dual sugar-binding lectin domain controls the substrate specificity of a mucin-type O-glycosyltransferase.

Collette, A.M., Hassan, S.A., Schmidt, S.I., Lara, A.J., Yang, W., Samara, N.L.

(2024) Sci Adv 10: eadj8829-eadj8829

PubMed: 38416819 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adj8829
Primary Citation Related Structures:
8V9Q

PubMed Abstract:
N-acetylgalactosaminyl-transferases (GalNAc-Ts) initiate mucin-type O-glycosylation, an abundant and complex posttranslational modification that regulates host-microbe interactions, tissue development, and metabolism. GalNAc-Ts contain a lectin domain consisting of three homologous repeats (α, β, and γ), where α and β can potentially interact with O-GalNAc on substrates to enhance activity toward a nearby acceptor Thr/Ser. The ubiquitous isoenzyme GalNAc-T1 modulates heart development, immunity, and SARS-CoV-2 infectivity, but its substrates are largely unknown. Here, we show that both α and β in GalNAc-T1 uniquely orchestrate the O-glycosylation of various glycopeptide substrates. The α repeat directs O-glycosylation to acceptor sites carboxyl-terminal to an existing GalNAc, while the β repeat directs O-glycosylation to amino-terminal sites. In addition, GalNAc-T1 incorporates α and β into various substrate binding modes to cooperatively increase the specificity toward an acceptor site located between two existing O-glycans. Our studies highlight a unique mechanism by which dual lectin repeats expand substrate specificity and provide crucial information for identifying the biological substrates of GalNAc-T1.

Organizational Affiliation

Structural Biochemistry Unit, NIDCR, NIH, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 137.16 kDa
Atom Count: 8,310
Modeled Residue Count: 987
Deposited Residue Count: 1,166
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polypeptide N-acetylgalactosaminyltransferase 1 soluble form	A, C [auth B]	559	Mus musculus	Mutation(s): 0 Gene Names: Galnt1 EC: 2.4.1.41
UniProt
Find proteins for O08912 (Mus musculus) Explore O08912 Go to UniProtKB: O08912
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O08912
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C [auth B]	Go to GlyGen: O08912-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-5AC	B [auth D], D [auth F], E [auth H]	16	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P98088 (Homo sapiens) Explore P98088 Go to UniProtKB: P98088
PHAROS: P98088 GTEx: ENSG00000215182
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P98088
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth D] Focus chain D [auth F] Focus chain E [auth H]	Go to GlyGen: P98088-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth X]	5		N-Glycosylation	Interactions Focus chain F [auth X] Interactions & Density Focus chain F [auth X]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	2		N-Glycosylation	Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP (Subject of Investigation/LOI) Query on UDP Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain H [auth A]	H [auth A], S [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain H [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B]
A2G (Subject of Investigation/LOI) Query on A2G Download:Ideal Coordinates CCD File SDF format, chain X [auth H] SDF format, chain W [auth F] SDF format, chain P [auth D] MOL2 format, chain X [auth H] MOL2 format, chain W [auth F] MOL2 format, chain P [auth D] mmCIF format, chain X [auth H] mmCIF format, chain W [auth F] mmCIF format, chain P [auth D]	P [auth D], W [auth F], X [auth H]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain P [auth D] Focus chain W [auth F] Focus chain X [auth H] Interactions & Density Focus chain P [auth D] Focus chain W [auth F] Focus chain X [auth H]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B]	T [auth B], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain T [auth B] Focus chain U [auth B]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain I [auth A] MOL2 format, chain O [auth A] MOL2 format, chain I [auth A] mmCIF format, chain O [auth A] mmCIF format, chain I [auth A]	I [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth A] Interactions & Density Focus chain I [auth A] Focus chain O [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], M [auth A], Q [auth D], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth D] Focus chain R [auth D]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain N [auth A]	N [auth A], V [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain N [auth A] Focus chain V [auth B]