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.


2dc1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:47, 13 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.9&#8491;</td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [https://pdbe.org/2dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [https://pdbe.org/2dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU]] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).
+
[https://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 20: Line 20:
</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=2dc1 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=2dc1 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
-
<div style="background-color:#fffaf0;">
 
-
== Publication Abstract from PubMed ==
 
-
The crystal structure of the highly thermostable L-aspartate dehydrogenase (L-aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidus L-aspDH was refined at a resolution of 1.9 A with a crystallographic R-factor of 21.7% (R(free) = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidus L-aspDH/NAD/citrate ternary complex and the Thermotoga maritima L-aspDH/NAD binary complex showed that A. fulgidus L-aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritima L-aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidus L-aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two L-aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to L-aspDH and of the molecular basis of the high thermostability of a hyperthermophilic L-aspDH.
 
- 
-
Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex.,Yoneda K, Sakuraba H, Tsuge H, Katunuma N, Ohshima T FEBS J. 2007 Aug;274(16):4315-25. Epub 2007 Jul 25. PMID:17651440<ref>PMID:17651440</ref>
 
- 
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
-
</div>
 
-
<div class="pdbe-citations 2dc1" style="background-color:#fffaf0;"></div>
 
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Arcfl]]
+
[[Category: Archaeoglobus fulgidus]]
-
[[Category: Aspartate dehydrogenase]]
+
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Ohshima, T]]
+
[[Category: Ohshima T]]
-
[[Category: Sakuraba, H]]
+
[[Category: Sakuraba H]]
-
[[Category: Tsuge, H]]
+
[[Category: Tsuge H]]
-
[[Category: Yoneda, K]]
+
[[Category: Yoneda K]]
-
[[Category: L-aspartate dehydrogenase]]
+
-
[[Category: Nad]]
+
-
[[Category: Oxidoreductase]]
+

Current revision

Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus

PDB ID 2dc1

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools