8VH8 | pdb_00008vh8

Crystal structure of heparosan synthase 2 from Pasteurella multocida at 2.85 A

PDB DOI: https://doi.org/10.2210/pdb8VH8/pdb

Classification: TRANSFERASE
Organism(s): Pasteurella multocida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-31 Released: 2024-09-04
Deposition Author(s): Pedersen, L.C., Liu, J., Stancanelli, E., krahn, J.M.
Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), Department of Health & Human Services (HHS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.223 (Depositor), 0.221 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (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

Structural and Functional Analysis of Heparosan Synthase 2 from Pasteurella multocida (PmHS2) to Improve the Synthesis of Heparin.

Stancanelli, E., Krahn, J.A., Viverette, E., Dutcher, R., Pagadala, V., Borgnia, M.J., Liu, J., Pedersen, L.C.

(2024) ACS Catal 14: 6577-6588

PubMed: 39990868 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acscatal.4c00677
Primary Citation Related Structures:
8VH7, 8VH8, 8VIW

PubMed Abstract:
Heparin is a widely used drug to treat thrombotic disorders in hospitals. Heparosan synthase 2 from Pasteurella multocida (PmHS2) is a key enzyme used for the chemoenzymatic synthesis of heparin oligosaccharides. It has both activities: glucosaminyl transferase activity and glucuronyl transferase activity; however, the mechanism to carry out the glyco-oligomerization is unknown. Here, we report crystal structures of PmHS2 constructs with bound uridine diphosphate (UDP) and a cryo-EM structure of PmHS2 in complex with UDP and a heptasaccharide (NS 7-mer) substrate. Using a LC-MC analytical method, we discovered the enzyme displays both a two-step concerted oligomerization mode and a distributive oligomerization mode depending on the non-reducing end of the starting oligosaccharide primer. Removal of 7 amino acid residues from the C-terminus results in an enzymatically active monomer instead of dimer and loses the concerted oligomerization mode of activity. In addition, the monomer construct can transfer N-acetyl glucosamine at a substrate concentration that is ∼7-fold higher than wildtype enzyme. It was also determined that an F529A mutant can transfer an N-sulfo glucosamine (GlcNS) saccharide from a previously inactive UDP-GlcNS donor. Performing the glyco-transfer reaction at a high substrate concentration and the capability of using unnatural donors are desirable to simplify the chemoenzymatic synthesis to prepare heparin-based therapeutics.

Organizational Affiliation

Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA.

Macromolecule Content

Total Structure Weight: 259.35 kDa
Atom Count: 16,707
Modeled Residue Count: 2,099
Deposited Residue Count: 2,208
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparosan synthase B	A, B, C, D	552	Pasteurella multocida	Mutation(s): 0 Gene Names: hssB
UniProt
Find proteins for Q5SGE1 (Pasteurella multocida) Explore Q5SGE1 Go to UniProtKB: Q5SGE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SGE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 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 H [auth A] SDF format, chain MA [auth D] SDF format, chain Z [auth C] SDF format, chain P [auth B] SDF format, chain OA [auth D] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth D] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth C]	BA [auth C] F [auth A] H [auth A] MA [auth D] N [auth B] BA [auth C], F [auth A], H [auth A], MA [auth D], N [auth B], OA [auth D], P [auth B], Z [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain BA [auth C] Focus chain F [auth A] Focus chain H [auth A] Focus chain MA [auth D] Focus chain N [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth C] Focus chain F [auth A] Focus chain H [auth A] Focus chain MA [auth D] Focus chain N [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Z [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain X [auth B] SDF format, chain DA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain X [auth B] MOL2 format, chain DA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain X [auth B] mmCIF format, chain DA [auth C]	DA [auth C], QA [auth D], R [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain QA [auth D] Focus chain R [auth B] Focus chain X [auth B] Interactions & Density Focus chain DA [auth C] Focus chain QA [auth D] Focus chain R [auth B] Focus chain X [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain Y [auth C] SDF format, chain LA [auth D] SDF format, chain G [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain NA [auth D] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain G [auth A]	AA [auth C] E [auth A] G [auth A] LA [auth D] M [auth B] AA [auth C], E [auth A], G [auth A], LA [auth D], M [auth B], NA [auth D], O [auth B], Y [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain E [auth A] Focus chain G [auth A] Focus chain LA [auth D] Focus chain M [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth C] Focus chain E [auth A] Focus chain G [auth A] Focus chain LA [auth D] Focus chain M [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain Y [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain TA [auth D] SDF format, chain U [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain UA [auth D] SDF format, chain SA [auth D] SDF format, chain RA [auth D] SDF format, chain JA [auth C] SDF format, chain IA [auth C] SDF format, chain HA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain JA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain JA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C]	EA [auth C] FA [auth C] GA [auth C] HA [auth C] IA [auth C] EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], RA [auth D], S [auth B], SA [auth D], TA [auth D], U [auth B], UA [auth D], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain RA [auth D] Focus chain S [auth B] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth B] Focus chain UA [auth D] Focus chain V [auth B] Focus chain W [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain Q [auth B] SDF format, chain PA [auth D] SDF format, chain I [auth A] MOL2 format, chain CA [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain I [auth A] mmCIF format, chain CA [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain I [auth A]	CA [auth C], I [auth A], PA [auth D], Q [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain I [auth A] Focus chain PA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain CA [auth C] Focus chain I [auth A] Focus chain PA [auth D] Focus chain Q [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.223 (Depositor), 0.221 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.57	α = 90
b = 118.57	β = 90
c = 262.356	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ZIC-ES102645
Department of Health & Human Services (HHS)	United States	R44GM142304
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	1R01HL094463-09