3b5q Structure and Function: Difference between revisions

From MDWiki
Jump to navigationJump to search
No edit summary
No edit summary
Line 1: Line 1:
== Arylsulfatase K structure==
== Arylsulfatase K structure==


[[Image:ASK.png]]
[[Image:ASK.png]]


''Figure 1: Arylsulfatase K as a heterodimer; 3b5q chain A and B''.
'''''Figure 1:''' Arylsulfatase K as a heterodimer; 3b5q chain A and B''.




Line 48: Line 47:
   16:  2rh6-B 24.2  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: Structurally related proteins. (No 1 and 2 are two chains of arylsulfatase K)''.
'''''Figure 4:''' Structurally related proteins. (No 1 and 2 are two chains of arylsulfatase K)''.





Revision as of 00:47, 7 June 2008

Arylsulfatase K structure

ASK.png

Figure 1: Arylsulfatase K as a heterodimer; 3b5q chain A and B.


Protein data bank profile characteris arylsulfatase as a hydrolase and a sulfatase. A Sulfatase hydrolyses sulfate esters bonds of substrates, including O-sulfates and N-sulfates as shown below.


ReactionASK.png


Sulfatases are enzymes,which hydrolyse sulfate ester bonds of substrates. These are categorised as EC 3.1.6. in enzyme classifications. Most of the family members has shown to contain a highly conserved cystine residue and a bivalent metal binding site.

Arylsulphatase A (ASA) is a lysosomal enzyme which hydrolyzes cerebroside sulphate. Arylsulphatase B (ASB),also a lysosomal enzyme, which hydrolyzes the sulphate ester group from N-acetylgalactosamine 4-sulphate group of dermatan sulphate.

Sequence conservation

MSA data revealed several highly conserved residues in the N-terminal region of all sequences aligned. These residues are shown below as an alignment of Arylsulfatase K with the sequence of human stroid sulfatase.

AlignmentN.png


Structural alignment

  • 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: Structurally related proteins. (No 1 and 2 are two chains of arylsulfatase K).


  • The function of highly related proteins were found using ProFunc


Arylsulfatase A has both sulfuric ester hydrolase and phosphoric monoester hydrolase activities and localised in lysosomes.
Steryl-sulfatase is a sulfuric ester hydrolase found in endoplasmin reticulums.


Arylsulfatase K (BT1596) Interactions with other proteins

Net.png


Input Protein

  • BT1596 Putative sulfatase yidJ (481 aa) of Bacteroides thetaiotaomicron.

Predicted Functional Partners

  • BT3796: Putative secreted sulfatase ydeN (518 aa).
  • BT1595 Transcription termination factor rho (722 aa).
  • BT1597 Two-component system sensor histidine kinase (539 aa).
  • BT3057 N-acetylgalactosamine-6-sulfatase (508 aa).
  • BT1598 Putative two-component system sensor histidine (655 aa).
  • BT3101 N-sulphoglucosamine sulphohydrolase (455 aa).
  • BT3489 Arylsulfatase B {UniProtKB/TrEMBL-Q8A219} (458 aa).



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

N-acetylgalactosamine-4- sulfatase (Arylsulfatase B) hydrolyse the sulfate ester group from N-acetylgalactosamine 4-sulfate of dermatine sulfate. Deficiency of ASB cause a rare mucopolysaccharidosis (MPS IV; Maroteaux-Lamy syndrome)

All these enzymes has generaly the same function, but acts on different substrate.


Finding the functional site and mechamism of action

Published data on catalytic activity of STS and ASA was found in literature search. Both STS and ASA shows a divalent metal binding site in the catalytic site, but th crystal structure of ASK doesn't show this. However, three out of four residues which provide oxygen ligans to hold the cation are conserved in ASK. They are shown highlighted in purple in STS-ASK alignment.

AlignmentN.png


The Aspartic acid (D) in 35th position of STS is immidiatly followed by a second D, which is substituted by Histidine (H) in ASK. But when the site chain organisation of two residues are examined, it is a possibility for one Nitrogen in five-member-ring to donate a lone pair to form a coordinate bond with a divalent cation. Therefore ASK active site may contain a divalent cation in biologycal situations.

Three out of five catalytic resideus were also conserved between ASK and STS ( shown highlighted in red). The characteristic Cystine residue of nearly all sulfatases in conserved in STS, but substituted by Serine (S) in ASK. Biologycally acive STS has C post translationally modified in to a Formylglycine (FG), and subsequiently to a Hydroxyformylglycine (HFG) during the reaction. The crystal structure doesn't show a FG in ASK structure, however this may be a result of inadequite resolution. The crystal structure has obtained at 2.4 A resolution while bond lenghts of C=O and C-O are 1.2 A and 1.4 A respectively. Further evidence from literature suggests that a subset of ASK found in bacteria including Bacteroides thetaiotamicron and Klebsiella pneumoneae use a S, post translationally modified to a FG, for the same cataltic action[[1]].Finally H290 of STS in not conserven in either ASK or ASA, but the 3D structure shows a different H in the colse proximity and this H in ASA is conserved in most ASA from different species.


ASAsite1.png


Figure 1: Catalytic site of Arylsulfatase A (ASA) with the Magnesium ion bound. However H229 is only conserved within Arylsulfatase A of different species.


ASKsite1.png

figure 2: Catalytic site of Arylsulfatase K (ASK) with conserved catalytic residues. Residues marked in grey are possible to be involved in divalent metal binding , while residues marked in magenta are highly conserved with those of Arylsulfatase A (ASA) and steroid sulfatase (STS). Histidine (H) shown in cyan is not strictly consetved in MSA, but the only available nucleophile in the close proximity.



psx300

.

Figure 6: Surface of the ASK N-terminal catalytic site. It is buried deep in the moleculae, conected to the exterior via a narrow passage. This feature is also conserved with the STS catalytic site which is connected to the exterior via a substrate path.


Conservation of the C-terminus

C-terminus of sulfatases are recognised to contain a substrate binding site, hence weakly conserved throughout the family due to the variation of types of substrates used. However, when the C-terminal regions in two sequence alignment of ASK and STN was looked at, the level of conservation was very high. Based on this evidence it is predicted, that STS and ASK shair substrates.

AlignmentC.png



Possible function and likely substrates of ASK

STS is a mmembrane bound enzyme, mostly founf in human placenta and skin fibroblasts. Itconverts sex-stroid precursors to ative estrogen and androgen, thereofre give a local suppley of these hormones (Ghosh, D., 2007). ASK is a water soluble enzyme localysed in ER of the cell. No tissue localization is specified to the data. however, Based on all the above evidence, the possible function ASK may be binding and activation of post translationally modified stroids in the ER lumen.





Click here to go Back