2pkm: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2pkm.jpg|left|200px]]<br /><applet load="2pkm" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2pkm, resolution 1.90&Aring;" />
'''Crystal structure of M tuberculosis Adenosine Kinase complexed with adenosine'''<br />


==Overview==
==Crystal structure of M tuberculosis Adenosine Kinase complexed with adenosine==
Adenosine kinase (ADK) catalyzes the phosphorylation of adenosine (Ado) to, adenosine monophosphate (AMP). It is part of the purine salvage pathway, that has been identified only in eukaryotes, with the single exception of, Mycobacterium spp. Whereas it is not clear if Mycobacterium tuberculosis, (Mtb) ADK is essential, it has been shown that the enzyme can selectively, phosphorylate nucleoside analogs to produce products toxic to the cell. We, have determined the crystal structure of Mtb ADK unliganded as well as, ligand (Ado) bound at 1.5- and 1.9-A resolution, respectively. The, structure of the binary complexes with the inhibitor 2-fluoroadenosine, (F-Ado) bound and with the adenosine 5'-(beta,gamma-methylene)triphosphate, (AMP-PCP) (non-hydrolyzable ATP analog) bound were also solved at 1.9-A, resolution. These four structures indicate that Mtb ADK is a dimer formed, by an extended beta sheet. The active site of the unliganded ADK is in an, open conformation, and upon Ado binding a lid domain of the protein, undergoes a large conformation change to close the active site. In the, closed conformation, the lid forms direct interactions with the substrate, and residues of the active site. Interestingly, AMP-PCP binding alone was, not sufficient to produce the closed state of the enzyme. The binding mode, of F-Ado was characterized to illustrate the role of additional, non-bonding interactions in Mtb ADK compared with human ADK.
<StructureSection load='2pkm' size='340' side='right'caption='[[2pkm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2pkm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKM FirstGlance]. <br>
</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</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=2pkm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pkm OCA], [https://pdbe.org/2pkm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pkm RCSB], [https://www.ebi.ac.uk/pdbsum/2pkm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pkm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ADOK_MYCTU ADOK_MYCTU] ATP dependent phosphorylation of adenosine to monophosphate derivatives (By similarity).
== 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/pk/2pkm_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=2pkm ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2PKM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=ADN:'>ADN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Adenosine_kinase Adenosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.20 2.7.1.20] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PKM OCA].
*[[Adenosine kinase 3D structures|Adenosine kinase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
High resolution crystal structures of Mycobacterium tuberculosis adenosine kinase: insights into the mechanism and specificity of this novel prokaryotic enzyme., Reddy MC, Palaninathan SK, Shetty ND, Owen JL, Watson MD, Sacchettini JC, J Biol Chem. 2007 Sep 14;282(37):27334-42. Epub 2007 Jun 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17597075 17597075]
[[Category: Large Structures]]
[[Category: Adenosine kinase]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: Owen JL]]
[[Category: Owen, J.L.]]
[[Category: Palaninathan SK]]
[[Category: Palaninathan, S.K.]]
[[Category: Reddy MCM]]
[[Category: Reddy, M.C.M.]]
[[Category: Sacchettini JC]]
[[Category: Sacchettini, J.C.]]
[[Category: Shetty ND]]
[[Category: Shetty, N.D.]]
[[Category: Watson MD]]
[[Category: Watson, M.D.]]
[[Category: ADN]]
[[Category: adenosine]]
[[Category: adenosine kinase]]
[[Category: mycobacterium tuberculosis]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:56:52 2008''

Latest revision as of 09:10, 21 February 2024

Crystal structure of M tuberculosis Adenosine Kinase complexed with adenosine

2pkm, resolution 1.90Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=2pkm&oldid=4062443"