8D3Z | pdb_00008d3z

Crystal structure of GalS1 in complex with Manganese from Populus trichocarpas

PDB DOI: https://doi.org/10.2210/pdb8D3Z/pdb

Classification: TRANSFERASE
Organism(s): Populus trichocarpa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-01 Released: 2023-03-15
Deposition Author(s): Pereira, J.H., Prabhakar, P.K., Urbanowicz, B.R., Adams, P.D.
Funding Organization(s): Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical insight into a modular beta-1,4-galactan synthase in plants.

Prabhakar, P.K., Pereira, J.H., Taujale, R., Shao, W., Bharadwaj, V.S., Chapla, D., Yang, J.Y., Bomble, Y.J., Moremen, K.W., Kannan, N., Hammel, M., Adams, P.D., Scheller, H.V., Urbanowicz, B.R.

(2023) Nat Plants 9: 486-500

PubMed: 36849618 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41477-023-01358-4
Primary Citation Related Structures:
8D3T, 8D3Z

PubMed Abstract:
Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the β-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.

Macromolecule Content

Total Structure Weight: 102.89 kDa
Atom Count: 6,928
Modeled Residue Count: 798
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactan synthase	A, B	424	Populus trichocarpa	Mutation(s): 0 EC: 2.4.1
UniProt
Find proteins for A0A2K2AMS7 (Populus trichocarpa) Explore A0A2K2AMS7 Go to UniProtKB: A0A2K2AMS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K2AMS7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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	D, F	7		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G46836GH GlyCosmos: G46836GH GlyGen: G46836GH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] M [auth B] H [auth A], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]