3F5F | pdb_00003f5f

Crystal structure of heparan sulfate 2-O-sulfotransferase from gallus gallus as a maltose binding protein fusion.

• PDB DOI: https://doi.org/10.2210/pdb3F5F/pdb

• Classification: Transport, Transferase
• Organism(s): Escherichia coli K-12, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-11-03 Released: 2008-12-16 
• Deposition Author(s): Bethea, H.N., Xu, D., Liu, J., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Redirecting the substrate specificity of heparan sulfate 2-O-sulfotransferase by structurally guided mutagenesis.

Bethea, H.N., Xu, D., Liu, J., Pedersen, L.C.

(2008) Proc Natl Acad Sci U S A 105: 18724-18729

• PubMed: 19022906 
• DOI: https://doi.org/10.1073/pnas.0806975105
• Primary Citation Related Structures: 
  3F5F


• PubMed Abstract: 
  

  Heparan sulfate (HS) is a polysaccharide involved in essential physiological functions from regulating cell growth to blood coagulation. HS biosynthesis involves multiple specialized sulfotransferases such as 2-O-sulfotransferase (2OST) that transfers the sulfo group to the 2-OH position of iduronic acid (IdoA) or glucuronic acid (GlcA) within HS. Here, we report the homotrimeric crystal structure of 2OST from chicken, in complex with 3'-phosphoadenosine 5'-phosphate. Structural based mutational analysis has identified amino acid residues that are responsible for substrate specificity. The mutant R189A only transferred sulfates to GlcA moieties within the polysaccharide whereas mutants Y94A and H106A preferentially transferred sulfates to IdoA units. Our results demonstrate the feasibility for manipulating the substrate specificity of 2OST to synthesize HS with unique sulfation patterns. This work will aid the development of an enzymatic approach to synthesize heparin-based therapeutics.

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Organizational Affiliation: 
• Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.06 kDa 
• Atom Count: 5,403 
• Modeled Residue Count: 656 
• Deposited Residue Count: 658 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1	A	658	Escherichia coli K-12, Gallus gallus This entity is chimeric	Mutation(s): 1  Gene Names: b4034, HS2ST, HS2ST1, JW3994, malE EC: 2.8.2
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q76KB1 (Gallus gallus) Explore Q76KB1  Go to UniProtKB:  Q76KB1
UniProt Groups	P0AEX9Q76KB1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	C [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.243 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.647	α = 90
b = 152.647	β = 90
c = 85.686	γ = 120

Software Package:

Software Name	Purpose
StructureStudio	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-16 
Deposition Author(s): Bethea, H.N., Xu, D., Liu, J., Pedersen, L.C.

Revision History  

• Version 1.0: 2008-12-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-23
  Changes: Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description
• Version 2.3: 2024-10-16
  Changes: Structure summary