Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 33.40 kDa 
• Atom Count: 2802 
• Residue Count: 281 
• Unique protein chains: 2

2AIK

Formylglycine generating enzyme C336S mutant covalently bound to substrate peptide LCTPSRA

• DOI: 10.2210/pdb2AIK/pdb

• Classification: HYDROLASE ACTIVATOR,PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2005-07-29 Released: 2005-12-13 
• Deposition Author(s): Roeser, D., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.174 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Literature

A general binding mechanism for all human sulfatases by the formylglycine-generating enzyme

Roeser, D., Preusser-Kunze, A., Schmidt, B., Gasow, K., Wittmann, J.G., Dierks, T., von Figura, K., Rudolph, M.G.

(2006) Proc Natl Acad Sci U S A 103: 81-86

• PubMed: 16368756 
• DOI: 10.1073/pnas.0507592102
• Primary Citation of Related Structures:  
  2AFT, 2AFY, 2AIK, 2AIJ, 2AII


• PubMed Abstract: 
  

The formylglycine (FGly)-generating enzyme (FGE) uses molecular oxygen to oxidize a conserved cysteine residue in all eukaryotic sulfatases to the catalytically active FGly. Sulfatases degrade and remodel sulfate esters, and inactivity of FGE results in multiple sulfatase deficiency, a fatal disease. The previously determined FGE crystal structure revealed two crucial cysteine residues in the active site, one of which was thought to be implicated in substrate binding. The other cysteine residue partakes in a novel oxygenase mechanism that does not rely on any cofactors. Here, we present crystal structures of the individual FGE cysteine mutants and employ chemical probing of wild-type FGE, which defined the cysteines to differ strongly in their reactivity. This striking difference in reactivity is explained by the distinct roles of these cysteine residues in the catalytic mechanism. Hitherto, an enzyme-substrate complex as an essential cornerstone for the structural evaluation of the FGly formation mechanism has remained elusive. We also present two FGE-substrate complexes with pentamer and heptamer peptides that mimic sulfatases. The peptides isolate a small cavity that is a likely binding site for molecular oxygen and could host reactive oxygen intermediates during cysteine oxidation. Importantly, these FGE-peptide complexes directly unveil the molecular bases of FGE substrate binding and specificity. Because of the conserved nature of FGE sequences in other organisms, this binding mechanism is of general validity. Furthermore, several disease-causing mutations in both FGE and sulfatases are explained by this binding mechanism.

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Organizational Affiliation: 

Department of Molecular Structural Biology, University of Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sulfatase modifying factor 1	X	286	Homo sapiens	Mutation(s): 1  Gene Names: SUMF1, PSEC0152, UNQ3037/PRO9852 EC: 1.8.3.7
Find proteins for Q8NBK3 (Homo sapiens) Explore Q8NBK3  Go to UniProtKB:  Q8NBK3
NIH Common Fund Data Resources
PHAROS:  Q8NBK3 GTEx:  ENSG00000144455

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LCTPSRA peptide from Arylsulfatase A	P	7	N/A	Mutation(s): 0
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: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	A	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	X	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	X	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.174 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.719	α = 90
b = 109.517	β = 90
c = 43.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-29 
• Released Date: 2005-12-13 
Deposition Author(s): Roeser, D., Rudolph, M.G.

Revision History 

• Version 1.0: 2005-12-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary