1NST

THE SULFOTRANSFERASE DOMAIN OF HUMAN HAPARIN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the sulfotransferase domain of human heparan sulfate N-deacetylase/ N-sulfotransferase 1.

Kakuta, Y.Sueyoshi, T.Negishi, M.Pedersen, L.C.

(1999) J.Biol.Chem. 274: 10673-10676


  • PubMed Abstract: 
  • Heparan sulfate N-deacetylase/N-sulfotransferase (HSNST) catalyzes the first and obligatory step in the biosynthesis of heparan sulfates and heparin. The crystal structure of the sulfotransferase domain (NST1) of human HSNST-1 has been determined at ...

    Heparan sulfate N-deacetylase/N-sulfotransferase (HSNST) catalyzes the first and obligatory step in the biosynthesis of heparan sulfates and heparin. The crystal structure of the sulfotransferase domain (NST1) of human HSNST-1 has been determined at 2.3-A resolution in a binary complex with 3'-phosphoadenosine 5'-phosphate (PAP). NST1 is approximately spherical with an open cleft, and consists of a single alpha/beta fold with a central five-stranded parallel beta-sheet and a three-stranded anti-parallel beta-sheet bearing an interstrand disulfide bond. The structural regions alpha1, alpha6, beta1, beta7, 5'-phosphosulfate binding loop (between beta1 and alpha1), and a random coil (between beta8 and alpha13) constitute the PAP binding site of NST1. The alpha6 and random coil (between beta2 and alpha2), which form an open cleft near the 5'-phosphate of the PAP molecule, may provide interactions for substrate binding. The conserved residue Lys-614 is in position to form a hydrogen bond with the bridge oxygen of the 5'-phosphate.


    Related Citations: 
    • A Role of Lys614 in the Sulfotransferase Activity of Human Heparan Sulfate N-Deacetylase/N-Sulfotransferase
      Sueyoshi, T.,Kakuta, Y.,Pedersen, L.C.,Wall, F.E.,Pedersen, L.G.,Negishi, M.
      (1998) FEBS Lett. 433: 211


    Organizational Affiliation

    Pharmacogenetics Section, Laboratory of Reproductive and Developmental Toxicology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEPARAN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE
A
325Homo sapiensGene Names: NDST1 (HSST, HSST1)
EC: 3.-.-.-, 2.8.2.8, 2.8.2.-
Find proteins for P52848 (Homo sapiens)
Go to Gene View: NDST1
Go to UniProtKB:  P52848
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P

Download SDF File 
Download CCD File 
A
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.417α = 90.00
b = 54.501β = 100.05
c = 68.938γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SHELX-96phasing
SHELX-96model building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELX-96refinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance