3kpd: Difference between revisions

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 ==Crystal Structure of the CBS domain pair of protein MJ0100 in complex with 5 -methylthioadenosine and S-adenosyl-L-methionine.==
-<StructureSection load='3kpd' size='340' side='right' caption='[[3kpd]], [[Resolution|resolution]] 2.91&Aring;' scene=''>
+<StructureSection load='3kpd' size='340' side='right'caption='[[3kpd]], [[Resolution|resolution]] 2.91&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3kpd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KPD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KPD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3kpd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KPD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KPD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.91&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kpb|3kpb]], [[3kpc|3kpc]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3kpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kpd OCA], [https://pdbe.org/3kpd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kpd RCSB], [https://www.ebi.ac.uk/pdbsum/3kpd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kpd ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kpd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kpd OCA], [http://pdbe.org/3kpd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kpd RCSB], [http://www.ebi.ac.uk/pdbsum/3kpd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kpd ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ASST_METJA ASST_METJA] Required for O-acetylhomoserine sulfhydrylase (OAHS)-independent homocysteine (Hcy) biosynthesis. Together with MJ0099, catalyzes the condensation of sulfide with aspartate semialdehyde to generate homocysteine. Likely functions through persulfide intermediate.[UniProtKB:Q8TPT4]
 == 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/kp/3kpd_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/3kpd_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </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=3kpd ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Cystathionine beta-synthase (CBS) domains are small motifs that are present in proteins with completely different functions. Several genetic diseases in humans have been associated with mutations in their sequence, which has made them promising targets for rational drug design. The protein MJ0100 from Methanocaldococcus jannaschii includes a DUF39 domain of so far unknown function and a CBS domain pair (Bateman domain) at its C-terminus. This work presents the crystallographic analysis of four different states of the CBS motif pair of MJ0100 in complex with different numbers of S-adenosyl-L-methionine (SAM) and S-methyl-5'-thioadenosine (MTA) ligands, providing evidence that ligand-induced conformational reorganization of Bateman domain dimers could be an important regulatory mechanism. These observations are in contrast to what is known from most of the other Bateman domain structures but are supported by recent studies on the magnesium transporter MgtE. Our structures represent the first example of a CBS domain protein complexed with SAM and/or MTA and might provide a structural basis for understanding the molecular mechanisms regulated by SAM upon binding to the C-terminal domain of human CBS, whose structure remains unknown.
-Binding of S-methyl-5'-thioadenosine and S-adenosyl-L-methionine to protein MJ0100 triggers an open-to-closed conformational change in its CBS motif pair.,Lucas M, Encinar JA, Arribas EA, Oyenarte I, Garcia IG, Kortazar D, Fernandez JA, Mato JM, Martinez-Chantar ML, Martinez-Cruz LA J Mol Biol. 2010 Feb 26;396(3):800-20. Epub 2009 Dec 21. PMID:20026078<ref>PMID:20026078</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3kpd" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 43067]]
+[[Category: Large Structures]]
-[[Category: Arribas, E A]]
+[[Category: Methanocaldococcus jannaschii]]
-[[Category: Encinar, J A]]
+[[Category: Arribas EA]]
-[[Category: Fernandez, J A]]
+[[Category: Encinar JA]]
-[[Category: Garcia, I G]]
+[[Category: Fernandez JA]]
-[[Category: Kortazar, D]]
+[[Category: Garcia IG]]
-[[Category: Lucas, M]]
+[[Category: Kortazar D]]
-[[Category: Martinez-Chantar, M L]]
+[[Category: Lucas M]]
-[[Category: Martinez-Cruz, L A]]
+[[Category: Martinez-Chantar ML]]
-[[Category: Mato, J M]]
+[[Category: Martinez-Cruz LA]]
-[[Category: Oyenarte, I]]
+[[Category: Mato JM]]
-[[Category: Cbs domain]]
+[[Category: Oyenarte I]]
-[[Category: Conformational change]]
-[[Category: S-adenosylmethionine]]
-[[Category: Unknown function]]