1wn6: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1wn6.gif|left|200px]]


<!--
==Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S==
The line below this paragraph, containing "STRUCTURE_1wn6", creates the "Structure Box" on the page.
<StructureSection load='1wn6' size='340' side='right'caption='[[1wn6]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1wn6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_terreus Aspergillus terreus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WN6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WN6 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARS:ARSENIC'>ARS</scene>, <scene name='pdbligand=BST:6-(4-AMINO-4-HYDROXY-2-OXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-3-[3-AMINO-5-(N-METHYL-GUANIDINO)-PENT+ANOYLAMINO]-3,6-DIHYDRO-2H-PYRAN-2-CARBOXYLIC+ACID'>BST</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
{{STRUCTURE_1wn6| PDB=1wn6 |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wn6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wn6 OCA], [https://pdbe.org/1wn6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wn6 RCSB], [https://www.ebi.ac.uk/pdbsum/1wn6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wn6 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/BSD_ASPTE BSD_ASPTE] Catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wn/1wn6_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wn6 ConSurf].
<div style="clear:both"></div>


'''Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S'''
==See Also==
 
*[[Deaminase 3D structures|Deaminase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
The set of blasticidin S (BS) and blasticidin S deaminase (BSD) is a widely used selectable marker for gene transfer experiments. BSD is a member of the cytidine deaminase (CDA) family; it is a zinc-dependent enzyme with three cysteines and one water molecule as zinc ligands. The crystal structures of BSD were determined in six states (i.e. native, substrate-bound, product-bound, cacodylate-bound, substrate-bound E56Q mutant, and R90K mutant). In the structures, the zinc position and coordination structures vary. The substrate-bound structure shows a large positional and geometrical shift of zinc with a double-headed electron density of the substrate that seems to be assigned to the amino and hydroxyl groups of the substrate and product, respectively. In this intermediate-like structure, the steric hindrance of the hydroxyl group pushes the zinc into the triangular plane consisting of three cysteines with a positional shift of approximately 0.6 A, and the fifth ligand water approaches the opposite direction of the substrate with a shift of 0.4 A. Accordingly, the zinc coordination is changed from tetrahedral to trigonal bipyramidal, and its coordination distance is extended between zinc and its intermediate. The shift of zinc and the recruited water is also observed in the structure of the inactivated E56Q mutant. This novel observation is different in two-cysteine cytidine deaminase Escherichia coli CDA and might be essential for the reaction mechanism in BSD, since it is useful for the easy release of the product by charge compensation and for the structural change of the substrate.
 
==About this Structure==
1WN6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_terreus Aspergillus terreus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WN6 OCA].
 
==Reference==
Crystal structures of blasticidin S deaminase (BSD): implications for dynamic properties of catalytic zinc., Kumasaka T, Yamamoto M, Furuichi M, Nakasako M, Teh AH, Kimura M, Yamaguchi I, Ueki T, J Biol Chem. 2007 Dec 21;282(51):37103-11. Epub 2007 Oct 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17959604 17959604]
[[Category: Aspergillus terreus]]
[[Category: Aspergillus terreus]]
[[Category: Blasticidin-S deaminase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Furuichi M]]
[[Category: Furuichi, M.]]
[[Category: Kimura M]]
[[Category: Kimura, M.]]
[[Category: Kumasaka T]]
[[Category: Kumasaka, T.]]
[[Category: Nakasako M]]
[[Category: Nakasako, M.]]
[[Category: Ueki T]]
[[Category: Ueki, T.]]
[[Category: Yamaguchi I]]
[[Category: Yamaguchi, I.]]
[[Category: Yamamoto M]]
[[Category: Yamamoto, M.]]
[[Category: Cytidine deaminase family]]
[[Category: Hydrolase]]
[[Category: Tetramer]]
[[Category: Zinc]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 30 13:22:25 2008''

Latest revision as of 16:32, 13 March 2024

Crystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin SCrystal Structure of Blasticidin S Deaminase (BSD) Complexed with Tetrahedral Intermediate of Blasticidin S

Structural highlights

1wn6 is a 2 chain structure with sequence from Aspergillus terreus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BSD_ASPTE Catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1wn6, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1wn6&oldid=4087851"