This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1wyv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:35, 13 March 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1wyv.png|left|200px]]
 
-
<!--
+
==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form==
-
The line below this paragraph, containing "STRUCTURE_1wyv", creates the "Structure Box" on the page.
+
<StructureSection load='1wyv' size='340' side='right'caption='[[1wyv]], [[Resolution|resolution]] 2.40&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'>[[1wyv]] is a 8 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=1WYV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WYV 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]] 2.4&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AOA:(AMINOOXY)ACETIC+ACID'>AOA</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-
{{STRUCTURE_1wyv| PDB=1wyv | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wyv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyv OCA], [https://pdbe.org/1wyv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wyv RCSB], [https://www.ebi.ac.uk/pdbsum/1wyv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyv ProSAT], [https://www.topsan.org/Proteins/RSGI/1wyv TOPSAN]</span></td></tr>
-
 
+
</table>
-
===Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form===
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/Q5SKW8_THET8 Q5SKW8_THET8] The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity).[HAMAP-Rule:MF_00712][SAAS:SAAS023010_004_045580]
-
 
+
== Evolutionary Conservation ==
-
<!--
+
[[Image:Consurf_key_small.gif|200px|right]]
-
The line below this paragraph, {{ABSTRACT_PUBMED_15791207}}, adds the Publication Abstract to the page
+
Check<jmol>
-
(as it appears on PubMed at http://www.pubmed.gov), where 15791207 is the PubMed ID number.
+
<jmolCheckbox>
-
-->
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyv_consurf.spt"</scriptWhenChecked>
-
{{ABSTRACT_PUBMED_15791207}}
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==About this Structure==
+
</jmolCheckbox>
-
1WYV is a 8 chains structure of sequences 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=1WYV OCA].
+
</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=1wyv ConSurf].
-
 
+
<div style="clear:both"></div>
-
==Reference==
+
__TOC__
-
Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia., Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N, EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15791207 15791207]
+
</StructureSection>
-
[[Category: Thermus thermophilus]]
+
[[Category: Large Structures]]
-
[[Category: Kamiya, N.]]
+
[[Category: Thermus thermophilus HB8]]
-
[[Category: Kuramitsu, S.]]
+
[[Category: Kamiya N]]
-
[[Category: Maoka, N.]]
+
[[Category: Kuramitsu S]]
-
[[Category: Masui, R.]]
+
[[Category: Maoka N]]
-
[[Category: Nakagawa, N.]]
+
[[Category: Masui R]]
-
[[Category: Nakai, T.]]
+
[[Category: Nakagawa N]]
-
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+
[[Category: Nakai T]]
-
[[Category: Riken structural genomics/proteomics initiative]]
+
-
[[Category: Rsgi]]
+
-
[[Category: Structural genomic]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Nov 16 17:06:56 2008''
+

Current revision

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in inhibitor-bound form

PDB ID 1wyv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wyv"
Personal tools