1wsv: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1wsv.png|left|200px]]
-<!--
+==Crystal Structure of Human T-protein of Glycine Cleavage System==
-The line below this paragraph, containing "STRUCTURE_1wsv", creates the "Structure Box" on the page.
+<StructureSection load='1wsv' size='340' side='right'caption='[[1wsv]], [[Resolution|resolution]] 2.60&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'>[[1wsv]] is a 2 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=1WSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WSV 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=THH:N-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC+ACID'>THH</scene></td></tr>
-{{STRUCTURE_1wsv|  PDB=1wsv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wsv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wsv OCA], [https://pdbe.org/1wsv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wsv RCSB], [https://www.ebi.ac.uk/pdbsum/1wsv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wsv ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN] Defects in AMT are a cause of non-ketotic hyperglycinemia (NKH) [MIM:[https://omim.org/entry/605899 605899]; also known as glycine encephalopathy (GCE). NKH is an autosomal recessive disease characterized by accumulation of a large amount of glycine in body fluid and by severe neurological symptoms.<ref>PMID:8005589</ref> <ref>PMID:9600239</ref> <ref>PMID:9621520</ref> <ref>PMID:10873393</ref> <ref>PMID:11286506</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/GCST_HUMAN GCST_HUMAN] The glycine cleavage system catalyzes the degradation of glycine.
+== 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/ws/1wsv_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=1wsv ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+T-protein, a component of the glycine cleavage system, catalyzes the formation of ammonia and 5,10-methylenetetrahydrofolate from the aminomethyl moiety of glycine attached to the lipoate cofactor of H-protein. Several mutations in the human T-protein gene cause non-ketotic hyperglycinemia. To gain insights into the effect of disease-causing mutations and the catalytic mechanism at the molecular level, crystal structures of human T-protein in free form and that bound to 5-methyltetrahydrofolate (5-CH3-H4folate) have been determined at 2.0 A and 2.6 A resolution, respectively. The overall structure consists of three domains arranged in a cloverleaf-like structure with the central cavity, where 5-CH3-H4folate is bound in a kinked shape with the pteridine group deeply buried into the hydrophobic pocket and the glutamyl group pointed to the C-terminal side surface. Most of the disease-related residues cluster around the cavity, forming extensive hydrogen bonding networks. These hydrogen bonding networks are employed in holding not only the folate-binding space but also the positions and the orientations of alpha-helix G and the following loop in the middle region, which seems to play a pivotal role in the T-protein catalysis. Structural and mutational analyses demonstrated that Arg292 interacts through water molecules with the folate polyglutamate tail, and that the invariant Asp101, located close to the N10 group of 5-CH3-H4folate, might play a key role in the initiation of the catalysis by increasing the nucleophilic character of the N10 atom of the folate substrate for the nucleophilic attack on the aminomethyl lipoate intermediate. A clever mechanism of recruiting the aminomethyl lipoate arm to the reaction site seems to function as a way of avoiding the release of toxic formaldehyde.
-===Crystal Structure of Human T-protein of Glycine Cleavage System===
+Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.,Okamura-Ikeda K, Hosaka H, Yoshimura M, Yamashita E, Toma S, Nakagawa A, Fujiwara K, Motokawa Y, Taniguchi H J Mol Biol. 2005 Sep 2;351(5):1146-59. PMID:16051266<ref>PMID:16051266</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1wsv" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16051266}}, adds the Publication Abstract to the page
+*[[Aminomethyltransferase 3D structures|Aminomethyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16051266 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16051266}}
+__TOC__
+</StructureSection>
-==About this Structure==
-WSV is a 2 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=1WSV OCA].
-==Reference==
-<ref group="xtra">PMID:16051266</ref><references group="xtra"/>
-[[Category: Aminomethyltransferase]]
 [[Category: Homo sapiens]]
-[[Category: Fujiwara, K.]]
+[[Category: Large Structures]]
-[[Category: Hosaka, H.]]
+[[Category: Fujiwara K]]
-[[Category: Motokawa, Y.]]
+[[Category: Hosaka H]]
-[[Category: Nakagawa, A.]]
+[[Category: Motokawa Y]]
-[[Category: Okamura-Ikeda, K.]]
+[[Category: Nakagawa A]]
-[[Category: Taniguchi, H.]]
+[[Category: Okamura-Ikeda K]]
-[[Category: Toma, S.]]
+[[Category: Taniguchi H]]
-[[Category: Yamashita, E.]]
+[[Category: Toma S]]
-[[Category: Yoshimura, M.]]
+[[Category: Yamashita E]]
-[[Category: Aminomethyl transferase]]
+[[Category: Yoshimura M]]
-[[Category: Glycine-cleavage sytem]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 15:53:45 2009''