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.


1ky8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:29, 14 February 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ky8.jpg|left|200px]]
 
-
{{Structure
+
==Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase==
-
|PDB= 1ky8 |SIZE=350|CAPTION= <scene name='initialview01'>1ky8</scene>, resolution 2.4&Aring;
+
<StructureSection load='1ky8' size='340' side='right'caption='[[1ky8]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> and <scene name='pdbligand=NAP:NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE'>NAP</scene>
+
<table><tr><td colspan='2'>[[1ky8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoproteus_tenax Thermoproteus tenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KY8 FirstGlance]. <br>
-
|ACTIVITY= [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(NADP(+)) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.9 1.2.1.9]
+
</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>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</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=1ky8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ky8 OCA], [https://pdbe.org/1ky8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ky8 RCSB], [https://www.ebi.ac.uk/pdbsum/1ky8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ky8 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GAPN_THETE GAPN_THETE] Catalyzes the irreversible NAD(P)-dependent non-phosphorylating oxidation of glyceraldehyde-3-phosphate (GAP) to 3-phosphoglycerate (3PG). It is highly specific for D-GAP.<ref>PMID:3121324</ref> <ref>PMID:9497334</ref>
 +
== 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/ky/1ky8_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=1ky8 ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase'''
+
==See Also==
-
 
+
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
-
 
+
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
-
==Overview==
+
== References ==
-
The NAD(+)-dependent non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) from the hyperthermophilic archaeum Thermoproteus tenax represents an archaeal member of the diverse superfamily of aldehyde dehydrogenases (ALDHs). GAPN catalyzes the irreversible oxidation of d-glyceraldehyde 3-phosphate to 3-phosphoglycerate. In this study, we present the crystal structure of GAPN in complex with its natural inhibitor NADP(+) determined by multiple anomalous diffraction methods. The structure was refined to a resolution of 2.4 A with an R-factor of 0.21. The overall fold of GAPN is similar to the structures of ALDHs described previously, consisting of three domains: a nucleotide-binding domain, a catalytic domain, and an oligomerization domain. Local differences in the active site are responsible for substrate specificity. The inhibitor NADP(+) binds at an equivalent site to the cosubstrate-binding site of other ALDHs and blocks the enzyme in its inactive state, possibly preventing the transition to the active conformation. Structural comparison between GAPN from the hyperthermophilic T. tenax and homologs of mesophilic organisms establishes several characteristics of thermostabilization. These include protection against heat-induced covalent modifications by reducing and stabilizing labile residues, a decrease in number and volume of empty cavities, an increase in beta-strand content, and a strengthening of subunit contacts by ionic and hydrophobic interactions.
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
1KY8 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermoproteus_tenax Thermoproteus tenax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KY8 OCA].
+
[[Category: Large Structures]]
-
 
+
-
==Reference==
+
-
The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax., Pohl E, Brunner N, Wilmanns M, Hensel R, J Biol Chem. 2002 May 31;277(22):19938-45. Epub 2002 Feb 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11842090 11842090]
+
-
[[Category: Glyceraldehyde-3-phosphate dehydrogenase (NADP(+))]]
+
-
[[Category: Single protein]]
+
[[Category: Thermoproteus tenax]]
[[Category: Thermoproteus tenax]]
-
[[Category: Brunner, N.]]
+
[[Category: Brunner N]]
-
[[Category: Hensel, R.]]
+
[[Category: Hensel R]]
-
[[Category: Pohl, E.]]
+
[[Category: Pohl E]]
-
[[Category: Wilmanns, M.]]
+
[[Category: Wilmanns M]]
-
[[Category: NA]]
+
-
[[Category: NAP]]
+
-
[[Category: aldh]]
+
-
[[Category: gapn]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:23:49 2008''
+

Current revision

Crystal Structure of the Non-phosphorylating glyceraldehyde-3-phosphate Dehydrogenase

PDB ID 1ky8

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/1ky8"
Personal tools