This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2amx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:13, 14 February 2024) (edit) (undo)
 
(12 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2amx.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076)==
-
|PDB= 2amx |SIZE=350|CAPTION= <scene name='initialview01'>2amx</scene>, resolution 2.02&Aring;
+
<StructureSection load='2amx' size='340' side='right'caption='[[2amx]], [[Resolution|resolution]] 2.02&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>
+
<table><tr><td colspan='2'>[[2amx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_yoelii Plasmodium yoelii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AMX FirstGlance]. <br>
-
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenosine_deaminase Adenosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.4 3.5.4.4] </span>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.02&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-
|DOMAIN=
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2amx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2amx OCA], [https://pdbe.org/2amx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2amx RCSB], [https://www.ebi.ac.uk/pdbsum/2amx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2amx ProSAT]</span></td></tr>
-
|RELATEDENTRY=
+
</table>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2amx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2amx OCA], [http://www.ebi.ac.uk/pdbsum/2amx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2amx RCSB]</span>
+
== Function ==
-
}}
+
[https://www.uniprot.org/uniprot/Q7RMV2_PLAYO Q7RMV2_PLAYO]
 +
== 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/am/2amx_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=2amx ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076)'''
+
==See Also==
-
 
+
*[[Adenosine deaminase 3D structures|Adenosine deaminase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the world. Advances in vaccine development and drug discovery are urgently needed to control these diseases and can be facilitated by production of purified recombinant proteins from Apicomplexan genomes and determination of their 3D structures. To date, both heterologous expression and crystallization of Apicomplexan proteins have seen only limited success. In an effort to explore the effectiveness of producing and crystallizing proteins on a genome-scale using a standardized methodology, over 400 distinct Plasmodium falciparum target genes were chosen representing different cellular classes, along with select orthologues from four other Plasmodium species as well as Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%) crystallized, culminating in 36 crystal structures. These results demonstrate that, contrary to previous findings, a standardized platform using Escherichia coli can be effective for genome-scale production and crystallography of Apicomplexan proteins. Predictably, orthologous proteins from different Apicomplexan genomes behaved differently in expression, purification and crystallization, although the overall success rates of Plasmodium orthologues do not differ significantly. Their differences were effectively exploited to elevate the overall productivity to levels comparable to the most successful ongoing structural genomics projects: 229 of the 468 target genes produced purified soluble protein from one or more organisms, with 80 and 32 of the purified targets, respectively, leading to crystals and ultimately structures from one or more orthologues.
+
[[Category: Large Structures]]
-
 
+
-
==About this Structure==
+
-
2AMX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_yoelii Plasmodium yoelii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AMX OCA].
+
-
 
+
-
==Reference==
+
-
Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms., Vedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, Mulichak A, Wernimont A, Bray J, Loppnau P, Plotnikova O, Newberry K, Sundararajan E, Houston S, Walker J, Tempel W, Bochkarev A, Kozieradzki I, Edwards A, Arrowsmith C, Roos D, Kain K, Hui R, Mol Biochem Parasitol. 2007 Jan;151(1):100-10. Epub 2006 Nov 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17125854 17125854]
+
-
[[Category: Adenosine deaminase]]
+
[[Category: Plasmodium yoelii]]
[[Category: Plasmodium yoelii]]
-
[[Category: Single protein]]
+
[[Category: Alam Z]]
-
[[Category: Alam, Z.]]
+
[[Category: Amani M]]
-
[[Category: Amani, M.]]
+
[[Category: Arrowsmith CH]]
-
[[Category: Arrowsmith, C H.]]
+
[[Category: Bochkarev A]]
-
[[Category: Bochkarev, A.]]
+
[[Category: Dong A]]
-
[[Category: Dong, A.]]
+
[[Category: Edwards AM]]
-
[[Category: Edwards, A M.]]
+
[[Category: Hui R]]
-
[[Category: Hui, R.]]
+
[[Category: Koeieradzki I]]
-
[[Category: Koeieradzki, I.]]
+
[[Category: Lew J]]
-
[[Category: Lew, J.]]
+
[[Category: Melone M]]
-
[[Category: Melone, M.]]
+
[[Category: Sundstrom M]]
-
[[Category: SGC, Structural Genomics Consortium.]]
+
[[Category: Vedadi M]]
-
[[Category: Sundstrom, M.]]
+
[[Category: Wasney G]]
-
[[Category: Vedadi, M.]]
+
[[Category: Weigelt J]]
-
[[Category: Wasney, G.]]
+
[[Category: Zhao Y]]
-
[[Category: Weigelt, J.]]
+
-
[[Category: Zhao, Y.]]
+
-
[[Category: plasmodium yoelii adenosine deaminase (py02076)]]
+
-
[[Category: sgc]]
+
-
[[Category: structural genomic]]
+
-
[[Category: structural genomics consortium]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:54:41 2008''
+

Current revision

Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076)

PDB ID 2amx

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/2amx"
Personal tools