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PDBsum entry 1hdh

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1hdh
Jmol
Contents
Protein chains
525 a.a. *
Ligands
SO4 ×8
Metals
_CA ×2
Waters ×810
* Residue conservation analysis
PDB id:
1hdh
Name: Hydrolase
Title: Arylsulfatase from pseudomonas aeruginosa
Structure: Arylsulfatase. Chain: a, b. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287. Strain: pao1s. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.30Å     R-factor:   0.199     R-free:   0.228
Authors: I.Boltes,H.Czapinska,A.Kahnert,R.V.Buelow,T.Dirks,B.Schmidt, K.V.Figura,M.A.Kertesz,I.Uson
Key ref:
I.Boltes et al. (2001). 1.3 A structure of arylsulfatase from Pseudomonas aeruginosa establishes the catalytic mechanism of sulfate ester cleavage in the sulfatase family. Structure, 9, 483-491. PubMed id: 11435113 DOI: 10.1016/S0969-2126(01)00609-8
Date:
16-Nov-00     Release date:   15-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P51691  (ARS_PSEAE) -  Arylsulfatase
Seq:
Struc:
 
Seq:
Struc:
536 a.a.
525 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.6.1  - Arylsulfatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phenol sulfate + H2O = a phenol + sulfate
phenol sulfate
+ H(2)O
= phenol
+
sulfate
Bound ligand (Het Group name = SO4)
corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00609-8 Structure 9:483-491 (2001)
PubMed id: 11435113  
 
 
1.3 A structure of arylsulfatase from Pseudomonas aeruginosa establishes the catalytic mechanism of sulfate ester cleavage in the sulfatase family.
I.Boltes, H.Czapinska, A.Kahnert, R.von Bülow, T.Dierks, B.Schmidt, K.von Figura, M.A.Kertesz, I.Usón.
 
  ABSTRACT  
 
BACKGROUND: Sulfatases constitute a family of enzymes with a highly conserved active site region including a Calpha-formylglycine that is posttranslationally generated by the oxidation of a conserved cysteine or serine residue. The crystal structures of two human arylsulfatases, ASA and ASB, along with ASA mutants and their complexes led to different proposals for the catalytic mechanism in the hydrolysis of sulfate esters. RESULTS: The crystal structure of a bacterial sulfatase from Pseudomonas aeruginosa (PAS) has been determined at 1.3 A. Fold and active site region are strikingly similar to those of the known human sulfatases. The structure allows a precise determination of the active site region, unequivocally showing the presence of a Calpha-formylglycine hydrate as the key catalytic residue. Furthermore, the cation located in the active site is unambiguously characterized as calcium by both its B value and the geometry of its coordination sphere. The active site contains a noncovalently bonded sulfate that occupies the same position as the one in para-nitrocatecholsulfate in previously studied ASA complexes. CONCLUSIONS: The structure of PAS shows that the resting state of the key catalytic residue in sulfatases is a formylglycine hydrate. These structural data establish a mechanism for sulfate ester cleavage involving an aldehyde hydrate as the functional group that initiates the reaction through a nucleophilic attack on the sulfur atom in the substrate. The alcohol is eliminated from a reaction intermediate containing pentacoordinated sulfur. Subsequent elimination of the sulfate regenerates the aldehyde, which is again hydrated. The metal cation involved in stabilizing the charge and anchoring the substrate during catalysis is established as calcium.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. A scheme of the Proposed Catalytic Mechanism

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 483-491) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19168632 D.Lu, M.E.Wörmann, X.Zhang, O.Schneewind, A.Gründling, and P.S.Freemont (2009).
Structure-based mechanism of lipoteichoic acid synthesis by Staphylococcus aureus LtaS.
  Proc Natl Acad Sci U S A, 106, 1584-1589.
PDB codes: 2w5q 2w5r 2w5s 2w5t
19726673 J.R.Myette, V.Soundararajan, J.Behr, Z.Shriver, R.Raman, and R.Sasisekharan (2009).
Heparin/heparan sulfate N-sulfamidase from Flavobacterium heparinum: structural and biochemical investigation of catalytic nitrogen-sulfur bond cleavage.
  J Biol Chem, 284, 35189-35200.  
19726671 J.R.Myette, V.Soundararajan, Z.Shriver, R.Raman, and R.Sasisekharan (2009).
Heparin/heparan sulfate 6-O-sulfatase from Flavobacterium heparinum: integrated structural and biochemical investigation of enzyme active site and substrate specificity.
  J Biol Chem, 284, 35177-35188.  
19229300 K.Schirner, J.Marles-Wright, R.J.Lewis, and J.Errington (2009).
Distinct and essential morphogenic functions for wall- and lipo-teichoic acids in Bacillus subtilis.
  EMBO J, 28, 830-842.
PDB code: 2w8d
19130455 M.A.Frese, and T.Dierks (2009).
Formylglycine aldehyde Tag--protein engineering through a novel post-translational modification.
  Chembiochem, 10, 425-427.  
19381802 M.Schenk, C.A.Koppisetty, D.C.Santos, E.Carmona, S.Bhatia, P.G.Nyholm, and N.Tanphaichitr (2009).
Interaction of arylsulfatase-A (ASA) with its natural sulfoglycolipid substrates: a computational and site-directed mutagenesis study.
  Glycoconj J, 26, 1029-1045.  
19086847 J.P.Lai, J.R.Thompson, D.S.Sandhu, and L.R.Roberts (2008).
Heparin-degrading sulfatases in hepatocellular carcinoma: roles in pathogenesis and therapy targets.
  Future Oncol, 4, 803-814.  
18178549 M.Mariappan, K.Radhakrishnan, T.Dierks, B.Schmidt, and K.von Figura (2008).
ERp44 mediates a thiol-independent retention of formylglycine-generating enzyme in the endoplasmic reticulum.
  J Biol Chem, 283, 6375-6383.  
18288656 P.Bojarová, E.Denehy, I.Walker, K.Loft, D.P.De Souza, L.W.Woo, B.V.Potter, M.J.McConville, and S.J.Williams (2008).
Direct evidence for ArO-S bond cleavage upon inactivation of Pseudomonas aeruginosa arylsulfatase by aryl sulfamates.
  Chembiochem, 9, 613-623.  
18625336 P.Bojarová, and S.J.Williams (2008).
Sulfotransferases, sulfatases and formylglycine-generating enzymes: a sulfation fascination.
  Curr Opin Chem Biol, 12, 573-581.  
18266766 S.L.Gande, M.Mariappan, B.Schmidt, T.H.Pringle, K.von Figura, and T.Dierks (2008).
Paralog of the formylglycine-generating enzyme--retention in the endoplasmic reticulum by canonical and noncanonical signals.
  FEBS J, 275, 1118-1130.  
18558715 T.L.Grove, K.H.Lee, J.St Clair, C.Krebs, and S.J.Booker (2008).
In vitro characterization of AtsB, a radical SAM formylglycine-generating enzyme that contains three [4Fe-4S] clusters.
  Biochemistry, 47, 7523-7538.  
17446859 E.Zito, M.Buono, S.Pepe, C.Settembre, I.Annunziata, E.M.Surace, T.Dierks, M.Monti, M.Cozzolino, P.Pucci, A.Ballabio, and M.P.Cosma (2007).
Sulfatase modifying factor 1 trafficking through the cells: from endoplasmic reticulum to the endoplasmic reticulum.
  EMBO J, 26, 2443-2453.  
17150269 P.Gadler, and K.Faber (2007).
New enzymes for biotransformations: microbial alkyl sulfatases displaying stereo- and enantioselectivity.
  Trends Biotechnol, 25, 83-88.  
16381585 J.Rush, and C.R.Bertozzi (2006).
An alpha-formylglycine building block for fmoc-based solid-phase peptide synthesis.
  Org Lett, 8, 131-134.  
16766528 O.Berteau, A.Guillot, A.Benjdia, and S.Rabot (2006).
A new type of bacterial sulfatase reveals a novel maturation pathway in prokaryotes.
  J Biol Chem, 281, 22464-22470.  
17045481 S.R.Hanson, L.J.Whalen, and C.H.Wong (2006).
Synthesis and evaluation of general mechanism-based inhibitors of sulfatases based on (difluoro)methyl phenyl sulfate and cyclic phenyl sulfamate motifs.
  Bioorg Med Chem, 14, 8386-8395.  
15657036 A.Preusser-Kunze, M.Mariappan, B.Schmidt, S.L.Gande, K.Mutenda, D.Wenzel, K.von Figura, and T.Dierks (2005).
Molecular characterization of the human Calpha-formylglycine-generating enzyme.
  J Biol Chem, 280, 14900-14910.  
16041070 D.Roeser, A.Dickmanns, K.Gasow, and M.G.Rudolph (2005).
De novo calcium/sulfur SAD phasing of the human formylglycine-generating enzyme using in-house data.
  Acta Crystallogr D Biol Crystallogr, 61, 1057-1066.
PDB code: 1z70
15708861 M.Mariappan, A.Preusser-Kunze, M.Balleininger, N.Eiselt, B.Schmidt, S.L.Gande, D.Wenzel, T.Dierks, and K.von Figura (2005).
Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme.
  J Biol Chem, 280, 15173-15179.  
15999201 S.R.Wallner, B.M.Nestl, and K.Faber (2005).
Highly enantioselective stereo-inverting sec-alkylsulfatase activity of hyperthermophilic Archaea.
  Org Biomol Chem, 3, 2652-2656.  
16161167 S.R.Wallner, M.Bauer, C.Würdemann, P.Wecker, F.O.Glöckner, and K.Faber (2005).
Highly enantioselective sec-alkyl sulfatase activity of the marine planctomycete Rhodopirellula baltica shows retention of configuration.
  Angew Chem Int Ed Engl, 44, 6381-6384.  
14749327 Q.Fang, J.Peng, and T.Dierks (2004).
Post-translational formylglycine modification of bacterial sulfatases by the radical S-adenosylmethionine protein AtsB.
  J Biol Chem, 279, 14570-14578.  
15493058 S.R.Hanson, M.D.Best, and C.H.Wong (2004).
Sulfatases: structure, mechanism, biological activity, inhibition, and synthetic utility.
  Angew Chem Int Ed Engl, 43, 5736-5763.  
12419807 C.Marquordt, Q.Fang, E.Will, J.Peng, K.von Figura, and T.Dierks (2003).
Posttranslational modification of serine to formylglycine in bacterial sulfatases. Recognition of the modification motif by the iron-sulfur protein AtsB.
  J Biol Chem, 278, 2212-2218.  
12526009 J.Peng, B.Schmidt, K.von Figura, and T.Dierks (2003).
Identification of formylglycine in sulfatases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
  J Mass Spectrom, 38, 80-86.  
14592974 K.Y.Cheng, E.D.Lowe, J.Sinclair, E.A.Nigg, and L.N.Johnson (2003).
The crystal structure of the human polo-like kinase-1 polo box domain and its phospho-peptide complex.
  EMBO J, 22, 5757-5768.
PDB codes: 1q4k 1q4o
12904291 S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, and M.Fischer (2003).
Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.
  J Biol Chem, 278, 42256-42265.
PDB codes: 1pvw 1pvy
12757705 T.Dierks, B.Schmidt, L.V.Borissenko, J.Peng, A.Preusser, M.Mariappan, and K.von Figura (2003).
Multiple sulfatase deficiency is caused by mutations in the gene encoding the human C(alpha)-formylglycine generating enzyme.
  Cell, 113, 435-444.  
12144918 J.D.Mougous, R.E.Green, S.J.Williams, S.E.Brenner, and C.R.Bertozzi (2002).
Sulfotransferases and sulfatases in mycobacteria.
  Chem Biol, 9, 767-776.  
11600503 J.Fey, M.Balleininger, L.V.Borissenko, B.Schmidt, K.von Figura, and T.Dierks (2001).
Characterization of posttranslational formylglycine formation by luminal components of the endoplasmic reticulum.
  J Biol Chem, 276, 47021-47028.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.