1ky8: Difference between revisions

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<StructureSection load='1ky8' size='340' side='right'caption='[[1ky8]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='1ky8' size='340' side='right'caption='[[1ky8]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ky8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35583 Atcc 35583]. 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>
<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>
</td></tr><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>
</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(NADP(+)) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+))], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.9 1.2.1.9] </span></td></tr>
<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>
<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>
</table>
== Function ==
== 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>
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:11842090<ref>PMID:11842090</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1ky8" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 35583]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Brunner, N]]
[[Category: Thermoproteus tenax]]
[[Category: Hensel, R]]
[[Category: Brunner N]]
[[Category: Pohl, E]]
[[Category: Hensel R]]
[[Category: Wilmanns, M]]
[[Category: Pohl E]]
[[Category: Aldh]]
[[Category: Wilmanns M]]
[[Category: Gapn]]
[[Category: Oxidoreductase]]

Latest revision as of 10:29, 14 February 2024

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

Structural highlights

1ky8 is a 1 chain structure with sequence from Thermoproteus tenax. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

References

  1. ↑ Hensel R, Laumann S, Lang J, Heumann H, Lottspeich F. Characterization of two D-glyceraldehyde-3-phosphate dehydrogenases from the extremely thermophilic archaebacterium Thermoproteus tenax. Eur J Biochem. 1987 Dec 30;170(1-2):325-33. PMID:3121324
  2. ↑ Brunner NA, Brinkmann H, Siebers B, Hensel R. NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase from Thermoproteus tenax. The first identified archaeal member of the aldehyde dehydrogenase superfamily is a glycolytic enzyme with unusual regulatory properties. J Biol Chem. 1998 Mar 13;273(11):6149-56. PMID:9497334

1ky8, resolution 2.40Å

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