1ypp

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:59, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ypp.gif|left|200px]]
 
-
{{Structure
+
==ACID ANHYDRIDE HYDROLASE==
-
|PDB= 1ypp |SIZE=350|CAPTION= <scene name='initialview01'>1ypp</scene>, resolution 2.4&Aring;
+
<StructureSection load='1ypp' size='340' side='right'caption='[[1ypp]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=PO4:PHOSPHATE ION'>PO4</scene>
+
<table><tr><td colspan='2'>[[1ypp]] is a 2 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=1YPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YPP FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
}}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ypp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ypp OCA], [https://pdbe.org/1ypp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ypp RCSB], [https://www.ebi.ac.uk/pdbsum/1ypp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ypp ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/IPYR_YEAST IPYR_YEAST]
 +
== 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/yp/1ypp_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=1ypp ConSurf].
 +
<div style="clear:both"></div>
-
'''ACID ANHYDRIDE HYDROLASE'''
+
==See Also==
-
 
+
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
The three-dimensional structure of the manganese-phosphate complex of inorganic pyrophosphatase from Saccharomyces cerevisiae has been refined to an R factor of 19.0% at 2.4-A resolution. X-ray data were collected from a single crystal using an imaging plate scanner and synchrotron radiation. There is one dimeric molecule in the asymmetric unit. The upper estimate of the root-mean-square coordinate error is 0.4 A using either the delta A plot or the superposition of the two crystallographically independent subunits. The good agreement between the coordinates of the two subunits, which were not subjected to non-crystallographic symmetry restraints, provides independent validation of the structure analysis. The active site in each subunit contains four manganese ions and two phosphates. The manganese ions are coordinated by the side chains of aspartate and glutamate residues. The phosphate groups, which were identified on the basis of their local stereochemistry, interact either directly or via water molecules with manganese ions and lysine, arginine, and tyrosine side chains. The phosphates are bridged by two of the manganese ions. The outer phosphate is exposed to solvent. The inner phosphate is surrounded by all four manganese ions. The ion-binding sites are related to the order of binding previously established from kinetic studies. A hypothesis for the transition state of the catalytic reaction is put forward.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
1YPP 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=1YPP OCA].
+
-
 
+
-
==Reference==
+
-
X-ray structure of yeast inorganic pyrophosphatase complexed with manganese and phosphate., Harutyunyan EH, Kuranova IP, Vainshtein BK, Hohne WE, Lamzin VS, Dauter Z, Teplyakov AV, Wilson KS, Eur J Biochem. 1996 Jul 1;239(1):220-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8706712 8706712]
+
-
[[Category: Inorganic diphosphatase]]
+
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Single protein]]
+
[[Category: Dauter Z]]
-
[[Category: Dauter, Z.]]
+
[[Category: Harutyunyan EH]]
-
[[Category: Harutyunyan, E H.]]
+
[[Category: Kuranova IP]]
-
[[Category: Kuranova, I P.]]
+
[[Category: Lamzin VS]]
-
[[Category: Lamzin, V S.]]
+
[[Category: Wilson KS]]
-
[[Category: Wilson, K S.]]
+
-
[[Category: MN]]
+
-
[[Category: PO4]]
+
-
[[Category: hydrolase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:25:55 2008''
+

Current revision

ACID ANHYDRIDE HYDROLASE

PDB ID 1ypp

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ypp"
Personal tools