2idx: Difference between revisions

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-{{Seed}}
-[[Image:2idx.png|left|200px]]
-<!--
+==Structure of Human ATP:Cobalamin adenosyltransferase bound to ATP.==
-The line below this paragraph, containing "STRUCTURE_2idx", creates the "Structure Box" on the page.
+<StructureSection load='2idx' size='340' side='right'caption='[[2idx]], [[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'>[[2idx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IDX 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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2idx|  PDB=2idx  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2idx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2idx OCA], [https://pdbe.org/2idx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2idx RCSB], [https://www.ebi.ac.uk/pdbsum/2idx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2idx ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/MMAB_HUMAN MMAB_HUMAN] Defects in MMAB are the cause of methylmalonic aciduria type cblB (MMAB) [MIM:[https://omim.org/entry/251110 251110]; also known as methylmalonic aciduria type B or vitamin B12-responsive methylmalonicaciduria of cblB complementation type. MMAB is a disorder of methylmalonate and cobalamin metabolism due to defective synthesis of adenosylcobalamin. Inheritance is autosomal recessive.<ref>PMID:12471062</ref> <ref>PMID:12514191</ref> <ref>PMID:15781192</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/MMAB_HUMAN MMAB_HUMAN]
+== 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/id/2idx_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=2idx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mutations in the gene encoding human ATP:cobalamin adenosyltransferase (hATR) can result in the metabolic disorder known as methylmalonic aciduria (MMA). This enzyme catalyzes the final step in the conversion of cyanocobalamin (vitamin B12) to the essential human cofactor adenosylcobalamin. Here we present the 2.5 A crystal structure of ATP bound to hATR refined to an Rfree value of 25.2%. The enzyme forms a tightly associated trimer, where the monomer comprises a five-helix bundle and the active sites lie on the subunit interfaces. Only two of the three active sites within the trimer contain the bound ATP substrate, thereby providing examples of apo- and substrate-bound-active sites within the same crystal structure. Comparison of the empty and occupied sites indicates that twenty residues at the enzyme's N-terminus become ordered upon binding of ATP to form a novel ATP-binding site and an extended cleft that likely binds cobalamin. The structure explains the role of 20 invariant residues; six are involved in ATP binding, including Arg190, which hydrogen bonds to ATP atoms on both sides of the scissile bond. Ten of the hydrogen bonds are required for structural stability, and four are in positions to interact with cobalamin. The structure also reveals how the point mutations that cause MMA are deficient in these functions.
-===Structure of Human ATP:Cobalamin adenosyltransferase bound to ATP.===
+Structure of ATP-bound human ATP:cobalamin adenosyltransferase.,Schubert HL, Hill CP Biochemistry. 2006 Dec 26;45(51):15188-96. PMID:17176040<ref>PMID:17176040</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17176040}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2idx" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17176040 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17176040}}
+__TOC__
+</StructureSection>
-==Disease==
-Known disease associated with this structure: Methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblB complementation type OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=607568 607568]]
-==About this Structure==
-IDX is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IDX OCA].
-==Reference==
-<ref group="xtra">PMID:17176040</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Hill, C P.]]
+[[Category: Large Structures]]
-[[Category: Schubert, H L.]]
+[[Category: Hill CP]]
-[[Category: Adenosyltransferase]]
+[[Category: Schubert HL]]
-[[Category: Atp]]
-[[Category: Cobalamin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:50:19 2009''