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.


1yba

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:20, 3 April 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1yba.gif|left|200px]]
 
-
{{Structure
+
==The active form of phosphoglycerate dehydrogenase==
-
|PDB= 1yba |SIZE=350|CAPTION= <scene name='initialview01'>1yba</scene>, resolution 2.24&Aring;
+
<StructureSection load='1yba' size='340' side='right'caption='[[1yba]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=AKG:2-OXYGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene> and <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
+
<table><tr><td colspan='2'>[[1yba]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YBA FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Phosphoglycerate_dehydrogenase Phosphoglycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.95 1.1.1.95]
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.24&#8491;</td></tr>
-
|GENE= serA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=1yba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yba OCA], [https://pdbe.org/1yba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yba RCSB], [https://www.ebi.ac.uk/pdbsum/1yba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yba ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SERA_ECOLI SERA_ECOLI]
 +
== 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/yb/1yba_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=1yba ConSurf].
 +
<div style="clear:both"></div>
-
'''The active form of phosphoglycerate dehydrogenase'''
+
==See Also==
-
 
+
*[[Phosphoglycerate dehydrogenase|Phosphoglycerate dehydrogenase]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
An active conformation of phosphoglycerate dehydrogenase (PGDH) from Escherichia coli has been obtained using X-ray crystallography. The X-ray crystal structure is used to examine the potential intermediates for V(max) regulation, for the redox reaction, and for cooperative effects of serine binding. The crystal structure at 2.2 A resolution contains bound NAD(+) cofactor, either sulfate or phosphate anions, and alpha-ketoglutarate, a nonphysiological substrate. A PGDH subunit is formed from three distinct domains: regulatory (RBD), substrate (SBD), and nucleotide binding (NBD). The crystal conformation of the homotetramer points to the fact that, in the absence of serine, coordinated movement of the RBD-SBD domains occurs relative to the NBD. The result is a conformational change involving the steric relationships of both the domains and the subunits. Within the active site of each subunit is a bound molecule of alpha-ketoglutarate and the coenzyme, NAD. The catalytic or active site cleft is changed slightly although it is still solvent exposed; therefore, the catalytic reaction probably involves additional conformational changes. By comparing the inhibited with the uninhibited complex, it is possible to describe changes in conformation that are involved in the inhibitory signal transduction of serine.
+
-
 
+
-
==About this Structure==
+
-
1YBA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YBA OCA].
+
-
 
+
-
==Reference==
+
-
Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase., Thompson JR, Bell JK, Bratt J, Grant GA, Banaszak LJ, Biochemistry. 2005 Apr 19;44(15):5763-73. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15823035 15823035]
+
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Phosphoglycerate dehydrogenase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Banaszak LJ]]
-
[[Category: Banaszak, L J.]]
+
[[Category: Thompson JR]]
-
[[Category: Thompson, J R.]]
+
-
[[Category: AKG]]
+
-
[[Category: NAD]]
+
-
[[Category: PO4]]
+
-
[[Category: UNK]]
+
-
[[Category: oxidoreductase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:20:40 2008''
+

Current revision

The active form of phosphoglycerate dehydrogenase

PDB ID 1yba

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/1yba"
Personal tools