8SND | pdb_00008snd

Chlorella virus Hyaluronan Synthase bound to GlcNAc primer and UDP-GlcA

PDB DOI: https://doi.org/10.2210/pdb8SND/pdb
EM Map EMD-40623: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Paramecium bursaria Chlorella virus CZ-2, Lama glama
Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
Mutation(s): Yes

Deposited: 2023-04-27 Released: 2024-05-01
Deposition Author(s): Stephens, Z., Zimmer, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural insights into translocation and tailored synthesis of hyaluronan.

Gorniak, I., Stephens, Z., Erramilli, S.K., Gawda, T., Kossiakoff, A.A., Zimmer, J.

(2025) Nat Struct Mol Biol 32: 161-171

PubMed: 39322765 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-024-01389-1
Primary Citation Related Structures:
8SMM, 8SMN, 8SMP, 8SNC, 8SND, 8SNE

PubMed Abstract:
Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) reaching several megadaltons in healthy tissues. HA is synthesized and translocated in a coupled reaction by HA synthase (HAS). Here, structural snapshots of HAS provide insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We monitor the extension of a GlcNAc primer with GlcA, reveal the coordination of the uridine diphosphate product by a conserved gating loop and capture the opening of a translocation channel to coordinate a translocating HA polymer. Furthermore, we identify channel-lining residues that modulate HA product lengths. Integrating structural and biochemical analyses suggests an avenue for polysaccharide engineering based on finely tuned enzymatic activity and HA coordination.

Organizational Affiliation

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.

Macromolecule Content

Total Structure Weight: 98.07 kDa
Atom Count: 6,090
Modeled Residue Count: 742
Deposited Residue Count: 845
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hyaluronan synthase	A	574	Paramecium bursaria Chlorella virus CZ-2	Mutation(s): 1 Gene Names: CZ-2_118R
UniProt
Find proteins for A0ACD6B8N5 (Paramecium bursaria Chlorella virus CZ-2) Explore A0ACD6B8N5 Go to UniProtKB: A0ACD6B8N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8N5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 872	B	134	Lama glama	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 881	C	137	Lama glama	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PE Query on 3PE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
UGA (Subject of Investigation/LOI) Query on UGA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID C₁₅ H₂₂ N₂ O₁₈ P₂ HDYANYHVCAPMJV-LXQIFKJMSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
Y01 Query on Y01 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Stephens, Z.

Zimmer, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144130
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM117372