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[[Image:1njr.gif|left|200px]]


{{Structure
==Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase==
|PDB= 1njr |SIZE=350|CAPTION= <scene name='initialview01'>1njr</scene>, resolution 1.9&Aring;
<StructureSection load='1njr' size='340' side='right'caption='[[1njr]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene>
<table><tr><td colspan='2'>[[1njr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJR FirstGlance]. <br>
|ACTIVITY=
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
|GENE= YMR087W or YM9582.12 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=XYL:D-XYLITOL'>XYL</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd02900 Macro_Appr_pase]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1njr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njr OCA], [https://pdbe.org/1njr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njr RCSB], [https://www.ebi.ac.uk/pdbsum/1njr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njr ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/1njr TOPSAN]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1njr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njr OCA], [http://www.ebi.ac.uk/pdbsum/1njr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1njr RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/YMX7_YEAST YMX7_YEAST] Highly specific phosphatase involved in the metabolism of ADP-ribose 1''-phosphate (Appr1p) which is produced as a consequence of tRNA splicing. + phosphate.
 
== Evolutionary Conservation ==
'''Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1njr_consurf.spt"</scriptWhenChecked>
Appr-1''-pase, an important and ubiquitous cellular processing enzyme involved in the tRNA splicing pathway, catalyzes the conversion of ADP-ribose-1''monophosphate (Appr-1''-p) to ADP-ribose. The structures of the native enzyme from the yeast and its complex with ADP-ribose were determined to 1.9 A and 2.05 A, respectively. Analysis of the three-dimensional structure of this protein, selected as a target in a structural genomics project, reveals its putative function and provides clues to the catalytic mechanism. The structure of the 284-amino acid protein shows a two-domain architecture consisting of a three-layer alphabetaalpha sandwich N-terminal domain connected to a small C-terminal helical domain. The structure of Appr-1''-pase in complex with the product, ADP-ribose, reveals an active-site water molecule poised for nucleophilic attack on the terminal phosphate group. Loop-region residues Asn 80, Asp 90, and His 145 may form a catalytic triad.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
1NJR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJR OCA].  
</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=1njr ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme., Kumaran D, Eswaramoorthy S, Studier FW, Swaminathan S, Protein Sci. 2005 Mar;14(3):719-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15722447 15722447]
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Single protein]]
[[Category: Burley SK]]
[[Category: Burley, S K.]]
[[Category: Eswaramoorthy S]]
[[Category: Eswaramoorthy, S.]]
[[Category: Kumaran D]]
[[Category: Kumaran, D.]]
[[Category: Studier FW]]
[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
[[Category: Swaminathan S]]
[[Category: Studier, F W.]]
[[Category: Swaminathan, S.]]
[[Category: dimer]]
[[Category: new york structural genomix research consortium]]
[[Category: nysgxrc]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomic]]
[[Category: two domain organization]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:31:19 2008''

Latest revision as of 11:50, 10 April 2024

Crystal structure of yeast ymx7, an ADP-ribose-1-monophosphataseCrystal structure of yeast ymx7, an ADP-ribose-1-monophosphatase

Structural highlights

1njr is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.9Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

YMX7_YEAST Highly specific phosphatase involved in the metabolism of ADP-ribose 1-phosphate (Appr1p) which is produced as a consequence of tRNA splicing. + phosphate.

Evolutionary Conservation

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

1njr, resolution 1.90Å

Drag the structure with the mouse to rotate

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OCA
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