3jqm: Difference between revisions

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[[Image:3jqm.png|left|200px]]


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==Binding of 5'-GTP to molybdenum cofactor biosynthesis protein MoaC from Thermus theromophilus HB8==
The line below this paragraph, containing "STRUCTURE_3jqm", creates the "Structure Box" on the page.
<StructureSection load='3jqm' size='340' side='right'caption='[[3jqm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3jqm]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JQM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3JQM FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
{{STRUCTURE_3jqm|  PDB=3jqm  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3jqm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3jqm OCA], [https://pdbe.org/3jqm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3jqm RCSB], [https://www.ebi.ac.uk/pdbsum/3jqm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3jqm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q5SHE1_THET8 Q5SHE1_THET8] Together with MoaA, is involved in the conversion of 5'-GTP to cyclic pyranopterin monophosphate (cPMP or molybdopterin precursor Z) (By similarity).[HAMAP-Rule:MF_01224][SAAS:SAAS002820_004_012265]
== 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/jq/3jqm_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=3jqm ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The first step in the molybdenum cofactor (Moco) biosynthesis pathway involves the conversion of guanosine triphosphate (GTP) to precursor Z by two proteins (MoaA and MoaC). MoaA belongs to the S-adenosylmethionine-dependent radical enzyme superfamily and is believed to generate protein and/or substrate radicals by reductive cleavage of S-adenosylmethionine using an Fe-S cluster. MoaC has been suggested to catalyze the release of pyrophosphate and the formation of the cyclic phosphate of precursor Z. However, structural evidence showing the binding of a substrate-like molecule to MoaC is not available. Here, apo and GTP-bound crystal structures of MoaC from Thermus thermophilus HB8 are reported. Furthermore, isothermal titration calorimetry experiments have been carried out in order to obtain thermodynamic parameters for the protein-ligand interactions. In addition, molecular-dynamics (MD) simulations have been carried out on the protein-ligand complex of known structure and on models of relevant complexes for which X-ray structures are not available. The biophysical, structural and MD results reveal the residues that are involved in substrate binding and help in speculating upon a possible mechanism.


===Binding of 5'-GTP to molybdenum cofactor biosynthesis protein MoaC from Thermus theromophilus HB8===
Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8.,Kanaujia SP, Jeyakanthan J, Nakagawa N, Balasubramaniam S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K Acta Crystallogr D Biol Crystallogr. 2010 Jul;66(Pt 7):821-33. Epub 2010 Jun 19. PMID:20606263<ref>PMID:20606263</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_20606263}}, adds the Publication Abstract to the page
<div class="pdbe-citations 3jqm" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20606263 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_20606263}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[3jqm]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3JQM OCA].
[[Category: Thermus thermophilus HB8]]
 
[[Category: Jeyakanthan J]]
==Reference==
[[Category: Kanaujia SP]]
<ref group="xtra">PMID:020606263</ref><references group="xtra"/>
[[Category: Kuramitsu S]]
[[Category: Thermus thermophilus]]
[[Category: Nakagawa N]]
[[Category: Jeyakanthan, J.]]
[[Category: Sekar K]]
[[Category: Kanaujia, S P.]]
[[Category: Shinkai A]]
[[Category: Kuramitsu, S.]]
[[Category: Yokoyama S]]
[[Category: Nakagawa, N.]]
[[Category: Rsgi, Riken Structural Genomics/Proteomics Initiative.]]
[[Category: Sekar, K.]]
[[Category: Shinkai, A.]]
[[Category: Yokoyama, S.]]
[[Category: Biosynthetic protein]]
[[Category: Moac]]
[[Category: Moco biosynthesis]]
[[Category: Molybdenum cofactor biosynthesis]]
[[Category: National project on protein structural and functional analyse]]
[[Category: Nppsfa]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rsgi]]
[[Category: Structural genomic]]

Latest revision as of 16:04, 1 November 2023

Binding of 5'-GTP to molybdenum cofactor biosynthesis protein MoaC from Thermus theromophilus HB8

3jqm, resolution 2.50Å

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