3bsqA Results: Difference between revisions

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'''MSA''' highlited sevlral residues in N-terminal region of the molecule which are highly conserved ''(figure 1)''.




'''Multiple sequence alignment (MSA)''' highlighted several residues in N-terminal region of the molecule which are highly conserved ‘‘ (figure 1)''.




[[Image:alignmentN.png]]


'''''Figure 1:''' Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty  of 5 and gap extension penalty of 2''.


 
    
 
 
 
The three dimentional structure of the enzyme was viewed using '''PyMol''' ''(figure 2)'' and these conserved residues were marked on the crystal structure. However they were not related to binding sited of Cl and Zn, but buried in the core of the protein within a pocket-like region ''(figure 3)''.
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some  technical probloems with '''PyMol'''.
 
Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.
 
 
 
   No:  Chain  Z    rmsd lali nres  %id  Description
  '''1:  3b5q-A 73.6  0.0  464  464  100  MOLECULE: PUTATIVE SULFATASE YIDJ;'''                                 
  '''2:  3b5q-B 70.2  0.3  464  467  100  MOLECULE: PUTATIVE SULFATASE YIDJ;'''                                 
  3:  2qzu-A 35.1  2.5  375  465  25  MOLECULE: PUTATIVE SULFATASE YIDJ;                                 
  4:  1fsu  28.7  2.8  344  474  22  MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE;                       
  5:  1n2l-A 28.4  3.0  343  483  25  MOLECULE: ARYLSULFATASE A;                                         
  6:  1n2k-A 28.3  3.2  344  482  25  MOLECULE: ARYLSULFATASE A;                                         
  7:  1e3c-P 28.2  3.2  344  481  26  MOLECULE: ARYLSULFATASE A;                                         
  8:  1e33-P 28.2  3.1  344  480  25  MOLECULE: ARYLSULFATASE A;                                         
  9:  1e2s-P 28.2  3.1  343  481  25  MOLECULE: ARYLSULFATASE A;                                         
  10:  1e1z-P 28.1  3.2  344  481  26  MOLECULE: ARYLSULFATASE A;                                         
  11:  1auk  27.9  3.1  343  481  25  MOLECULE: ARYLSULFATASE A; 
 
Figure 4: Structurally related proteins. (No 1 and 2 are two chains of arylsulfatase K).
 
 
The function of highly related proteins were found using [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/profunc/GetResults.pl?source=profunc&user_id=bw28&code=091700 ProFunc].
'''Putative Sulfatase YIDI''' hydrolyses sulfuric ester bonds of its substrate hence significant in metabolism. '''Arylsulfatase A''' has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities.
 
 
 
 
'''Protein interactions''' of arylsulfatase K with other proteis were viewed usig the programme '''STRING''', which revealed four major hits depending on 'neighbourhood', 'cooccurreance' and 'homology' evidence. 'Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that their genes are located in close proximity. But three of other proteins showed both cooccurrence and homology evidence, therefore their functions were analysed with '''ProFunc'''.
 
'''N-acetylgalactosamine-6-sulfatase''' cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate. '''N-sulphoglucosamine sulphohydrolase''' is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.
 
:'''N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate'''
 
 
 
'''Multiple sequence alignment (MSA)''' highlighted several residues in N-terminal region of the molecule which are highly conserved ‘‘ (figure 1)''. The three dimentional structure of the enzyme given in Protein data bank (PDB)  was viewed using '''PyMol''' ''(figure 2)'' and these conserved residues were marked on the crystal structure. However they were not in close proximity to the Zn binding site, but buried in the core of the protein within a pocket-like region ''(figure 3)''. 
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.
All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with '''PyMol'''. Three dimentional structure of arylsulfatase was aligned with other available structures using '''DALI''' server [http://ekhidna.biocenter.helsinki.fi/dali_server/results/20080513-017-30c6150342a20dabd7c2488208032bb4 (structural alignment)]. Results are shown in 'figure 4'.


Revision as of 03:07, 7 June 2008


Multiple sequence alignment (MSA) highlighted several residues in N-terminal region of the molecule which are highly conserved ‘‘ (figure 1).


AlignmentN.png

Figure 1: Two sequence alignment of ASK with STS using 'SIM' server, alignment methode' BLOSUM62' with gap penalty of 5 and gap extension penalty of 2.


All attempts to see the electrostatic nature of this pocket were unsuccessful, due to some technical probloems with PyMol. Three dimentional structure of arylsulfatase was aligned with other available structures using DALI server (structural alignment). Results are shown in 'figure 4'.

No: Chain Z rmsd lali nres %id Description 

  1:  3b5q-A 73.6  0.0  464   464  100   MOLECULE: PUTATIVE SULFATASE YIDJ;                                   
  2:  3b5q-B 70.2  0.3  464   467  100   MOLECULE: PUTATIVE SULFATASE YIDJ;                                   
  3:  2qzu-A 35.1  2.5  375   465   25   MOLECULE: PUTATIVE SULFATASE YIDJ;                                   
  4:  1fsu   28.7  2.8  344   474   22   MOLECULE: N-ACETYLGALACTOSAMINE-4-SULFATASE;                         
  5:  1n2l-A 28.4  3.0  343   483   25   MOLECULE: ARYLSULFATASE A;                                           
  6:  1n2k-A 28.1  3.1  342   482   25   MOLECULE: ARYLSULFATASE A;                                           
  7:  1e2s-P 28.1  3.0  341   481   26   MOLECULE: ARYLSULFATASE A;                                           
  8:  1e3c-P 28.0  3.1  341   481   26   MOLECULE: ARYLSULFATASE A;                                           
  9:  1e33-P 28.0  3.1  342   480   25   MOLECULE: ARYLSULFATASE A;                                           
 10:  1e1z-P 27.9  3.0  341   481   26   MOLECULE: ARYLSULFATASE A;                                           
 11:  1auk   27.8  3.1  340   481   26   MOLECULE: ARYLSULFATASE A;                                           
 12:  1p49-A 27.7  2.9  338   548   24   MOLECULE: STERYL-SULFATASE;                                          
 13:  1hdh-B 27.4  3.1  365   525   23   MOLECULE: ARYLSULFATASE;                                             
 14:  1hdh-A 27.4  3.0  363   525   23   MOLECULE: ARYLSULFATASE;                                             
 15:  2rh6-A 24.3  2.6  257   382   14   MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE;              
 16:  2rh6-B 24.2  2.6  257   382   14   MOLECULE: PHOSPHODIESTERASE-NUCLEOTIDE PYROPHOSPHATASE;

figure 4: Structural alighment of ASK. 3b5qA and B are two chains of ASK dimer and thired is ASK of Bacterioides fragilis.N-acetylgalactosamine -4- sulfatase, Arylsulfatase A and steryl sulfatase, also known as stroid sulfatase (STS) are most similar protein in structure to ASK. 1hdf is the ASK of Pseudomonal auruginosa.


Subcellular interactions of arylsulfatase K were searched usnig the programme STRING, based on 'neighbourhood', 'cooccurreance' and 'homology' evidence. ‘Putative secreted sulfatase ydeN' only showed neignbourhood relationship, which means that two genes are located in close proximity. In contrast, three of other proteins showed both cooccurrence and homology evidence.

The function of highly related proteins was searched using ProFunc.

Putative Sulfatase YIDI shows sulfuric ester hydrolase activity. Arylsulfatase A possesses phosphoric monester hydrolase activity as well as sulfuric ester hydrolase activity.


N-acetylgalactosamine-6-sulfatase cleaves the 6-sulfate groups of N-acetyl-D-galactosamine 6-sulfate units in chondroitin sulfate and D-galactose 6-sulfate units in keratan sulfate. N-sulphoglucosamine sulphohydrolase is also known as heparine sulfamidase, which catalyses the hydrolysis of Sulfur-Nitrogen bonds. N-sulphoglucosamine sulphohydrolase is responsible for the degradation of glucosaminlglycan and glycan structure of extra cellular matrix.

N-sulfo-D-glucosamine + H(2)O <=> D-glucosamine + sulfate
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