Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 52.72 kDa 
• Atom Count: 3700 
• Residue Count: 482 
• Unique protein chains: 1

1N2K

Crystal structure of a covalent intermediate of endogenous human arylsulfatase A

• DOI: 10.2210/pdb1N2K/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2002-10-23 Released: 2003-12-23 
• Deposition Author(s): Chruszcz, M., Laidler, P., Monkiewicz, M., Ortlund, E., Lebioda, L., Lewinski, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 

Literature

Crystal structure of a covalent intermediate of endogenous human arylsulfatase A.

Chruszcz, M., Laidler, P., Monkiewicz, M., Ortlund, E., Lebioda, L., Lewinski, K.

(2003) J Inorg Biochem 96: 386-392

• PubMed: 12888274 
• DOI: 10.1016/s0162-0134(03)00176-4
• Primary Citation of Related Structures:  
  1N2L, 1N2K


• PubMed Abstract: 
  

The structures of human arylsulfatase A crystals soaked in solutions containing 4-methylumbelliferyl phosphate and O-phospho-DL-tyrosine have been determined at 2.7- and 3.2-A resolution, respectively. The formylglycine in position 69, a residue crucial for catalytic activity, was unambiguously identified in both structures as forming a covalent bond to the phosphate moiety. A hydroxyl group is present at the Cbeta of residue 69 and the formation of one out of two possible stereomeric forms is strongly favoured. The structures confirm the importance of the gem-diol intermediate in the arylsulfatase's catalytic mechanism. The presence of an apparently stable covalent bond is consistent with the weak phosphatase activity observed for human arylsulfatase A. The structures of the complexes suggest that phosphate ions and phosphate esters inhibit arylsulfatase in non-covalent and covalent modes, respectively. The metal ion present in the active site of arylsulfatase A isolated from human placenta is Ca(2+) and not Mg(2+) as was found in the structure of the recombinant enzyme.

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Organizational Affiliation: 

Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060, Krakow, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARYLSULFATASE A	A	489	Homo sapiens	Mutation(s): 1  Gene Names: ARSA EC: 3.1.6.8
Find proteins for P15289 (Homo sapiens) Explore P15289  Go to UniProtKB:  P15289
NIH Common Fund Data Resources
PHAROS:  P15289 GTEx:  ENSG00000100299

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FGP	A	L-PEPTIDE LINKING	C3 H8 N O7 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.202 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.52	α = 90
b = 131.52	β = 90
c = 192.17	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-23 
• Released Date: 2003-12-23 
Deposition Author(s): Chruszcz, M., Laidler, P., Monkiewicz, M., Ortlund, E., Lebioda, L., Lewinski, K.

Revision History 

• Version 1.0: 2003-12-23
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-07-04
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary