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.


2vib

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:21, 13 December 2023) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2vib.jpg|left|200px]]
 
-
{{Structure
+
==Crystal structure of S172AbsSHMT obtained in the presence of L-allo- Thr==
-
|PDB= 2vib |SIZE=350|CAPTION= <scene name='initialview01'>2vib</scene>, resolution 1.85&Aring;
+
<StructureSection load='2vib' size='340' side='right'caption='[[2vib]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-
|SITE= <scene name='pdbsite=AC1:Plp+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:GLY+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Mpd+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Mpd+Binding+Site+For+Chain+A'>AC4</scene> and <scene name='pdbsite=AC5:Po4+Binding+Site+For+Chain+A'>AC5</scene>
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene> and <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
+
<table><tr><td colspan='2'>[[2vib]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VIB FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Glycine_hydroxymethyltransferase Glycine hydroxymethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.2.1 2.1.2.1]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2vib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vib OCA], [https://pdbe.org/2vib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vib RCSB], [https://www.ebi.ac.uk/pdbsum/2vib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vib ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q7SIB6_GEOSE Q7SIB6_GEOSE] Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.[HAMAP-Rule:MF_00051]
 +
== 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/vi/2vib_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=2vib ConSurf].
 +
<div style="clear:both"></div>
-
'''CRYSTAL STRUCTURE OF S172ABSSHMT OBTAINED IN THE PRESENCE OF L-ALLO-THR'''
+
==See Also==
-
 
+
*[[Serine hydroxymethyltransferase 3D structures|Serine hydroxymethyltransferase 3D structures]]
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
2VIB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VIB OCA].
+
[[Category: Geobacillus stearothermophilus]]
[[Category: Geobacillus stearothermophilus]]
-
[[Category: Glycine hydroxymethyltransferase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Appaji Rao N]]
-
[[Category: Bhavani, B S.]]
+
[[Category: Bhavani BS]]
-
[[Category: Murthy, M R.N.]]
+
[[Category: Murthy MRN]]
-
[[Category: Prakash, V.]]
+
[[Category: Prakash V]]
-
[[Category: Rajaram, V.]]
+
[[Category: Rajaram V]]
-
[[Category: Rao, N Appaji.]]
+
[[Category: Savithri HS]]
-
[[Category: Savithri, H S.]]
+
-
[[Category: GLY]]
+
-
[[Category: MPD]]
+
-
[[Category: PO4]]
+
-
[[Category: one-carbon metabolism]]
+
-
[[Category: plp-dependent]]
+
-
[[Category: pyridoxal phosphate]]
+
-
[[Category: serine hydroxymethyltransferase]]
+
-
[[Category: transferase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:46:54 2008''
+

Current revision

Crystal structure of S172AbsSHMT obtained in the presence of L-allo- Thr

PDB ID 2vib

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/2vib"
Personal tools