3c9t: Difference between revisions

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New page: left|200px {{Structure |PDB= 3c9t |SIZE=350|CAPTION= <scene name='initialview01'>3c9t</scene>, resolution 2.600Å |SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+...
 
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{{Structure
==AaThiL complexed with AMPPCP and TMP==
|PDB= 3c9t |SIZE=350|CAPTION= <scene name='initialview01'>3c9t</scene>, resolution 2.600&Aring;
<StructureSection load='3c9t' size='340' side='right'caption='[[3c9t]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+For+Residue+A+309'>AC1</scene>, <scene name='pdbsite=AC2:Mg+Binding+Site+For+Residue+A+310'>AC2</scene>, <scene name='pdbsite=AC3:Mg+Binding+Site+For+Residue+B+311'>AC3</scene>, <scene name='pdbsite=AC4:Mg+Binding+Site+For+Residue+A+312'>AC4</scene>, <scene name='pdbsite=AC5:Mg+Binding+Site+For+Residue+A+313'>AC5</scene>, <scene name='pdbsite=AC6:Mg+Binding+Site+For+Residue+A+314'>AC6</scene>, <scene name='pdbsite=AC7:Mg+Binding+Site+For+Residue+B+310'>AC7</scene>, <scene name='pdbsite=AC8:Mg+Binding+Site+For+Residue+B+312'>AC8</scene>, <scene name='pdbsite=AC9:Mg+Binding+Site+For+Residue+B+313'>AC9</scene>, <scene name='pdbsite=BC1:Mg+Binding+Site+For+Residue+B+314'>BC1</scene>, <scene name='pdbsite=BC2:Acp+Binding+Site+For+Residue+B+307'>BC2</scene>, <scene name='pdbsite=BC3:Tps+Binding+Site+For+Residue+A+308'>BC3</scene>, <scene name='pdbsite=BC4:Acp+Binding+Site+For+Residue+A+307'>BC4</scene> and <scene name='pdbsite=BC5:Tps+Binding+Site+For+Residue+B+308'>BC5</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPS:THIAMIN+PHOSPHATE'>TPS</scene> and <scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER'>ACP</scene>
<table><tr><td colspan='2'>[[3c9t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C9T FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/Thiamine-phosphate_kinase Thiamine-phosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.16 2.7.4.16]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
|GENE= thiL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 Aquifex aeolicus])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPS:THIAMIN+PHOSPHATE'>TPS</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=3c9t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c9t OCA], [https://pdbe.org/3c9t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c9t RCSB], [https://www.ebi.ac.uk/pdbsum/3c9t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c9t ProSAT]</span></td></tr>
 
</table>
'''AaThiL complexed with AMPPCP and TMP'''
== Evolutionary Conservation ==
 
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
==Overview==
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/3c9t_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3c9t ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Thiamin monophosphate kinase (ThiL) catalyzes the ATP-dependent phosphorylation of thiamin monophosphate (TMP) to form thiamin pyrophosphate (TPP), the active form of vitamin B 1. ThiL is a member of a small ATP binding superfamily that also includes the purine biosynthetic enzymes, PurM and PurL, NiFe hydrogenase maturation protein, HypE, and selenophosphate synthase, SelD. The latter four enzymes are believed to utilize phosphorylated intermediates during catalysis. To understand the mechanism of ThiL and its relationship to the other superfamily members, we determined the structure of Aquifex aeolicus ThiL (AaThiL) with nonhydrolyzable AMP-PCP and TMP, and also with the products of the reaction, ADP and TPP. The results suggest that AaThiL utilizes a direct, inline transfer of the gamma-phosphate of ATP to TMP rather than a phosphorylated enzyme intermediate. The structure of ThiL is compared to those of PurM, PurL, and HypE, and the ATP binding site is compared to that of PurL, for which nucleotide complexes are available.
Thiamin monophosphate kinase (ThiL) catalyzes the ATP-dependent phosphorylation of thiamin monophosphate (TMP) to form thiamin pyrophosphate (TPP), the active form of vitamin B 1. ThiL is a member of a small ATP binding superfamily that also includes the purine biosynthetic enzymes, PurM and PurL, NiFe hydrogenase maturation protein, HypE, and selenophosphate synthase, SelD. The latter four enzymes are believed to utilize phosphorylated intermediates during catalysis. To understand the mechanism of ThiL and its relationship to the other superfamily members, we determined the structure of Aquifex aeolicus ThiL (AaThiL) with nonhydrolyzable AMP-PCP and TMP, and also with the products of the reaction, ADP and TPP. The results suggest that AaThiL utilizes a direct, inline transfer of the gamma-phosphate of ATP to TMP rather than a phosphorylated enzyme intermediate. The structure of ThiL is compared to those of PurM, PurL, and HypE, and the ATP binding site is compared to that of PurL, for which nucleotide complexes are available.


==About this Structure==
Structural studies of thiamin monophosphate kinase in complex with substrates and products(,).,McCulloch KM, Kinsland C, Begley TP, Ealick SE Biochemistry. 2008 Mar 25;47(12):3810-21. Epub 2008 Mar 1. PMID:18311927<ref>PMID:18311927</ref>
3C9T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9T OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural studies of thiamin monophosphate kinase in complex with substrates and products(,)., McCulloch KM, Kinsland C, Begley TP, Ealick SE, Biochemistry. 2008 Mar 25;47(12):3810-21. Epub 2008 Mar 1. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18311927 18311927]
</div>
<div class="pdbe-citations 3c9t" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Thiamine-phosphate kinase]]
[[Category: Begley TP]]
[[Category: Begley, T P.]]
[[Category: Ealick SE]]
[[Category: Ealick, S E.]]
[[Category: Kinsland C]]
[[Category: Kinsland, C.]]
[[Category: McCulloch KM]]
[[Category: McCulloch, K M.]]
[[Category: ACP]]
[[Category: MG]]
[[Category: TPS]]
[[Category: alpha-beta structure]]
[[Category: beta barrel]]
[[Category: kinase]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:03:11 2008''

Latest revision as of 01:40, 21 November 2024

AaThiL complexed with AMPPCP and TMP

3c9t, resolution 2.60Å

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