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.

1h2h

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of TM1643

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1h2h"

@@ Line 1: / Line 1: @@
-[[Image:1h2h.gif|left|200px]]
- {{Structure
+==Crystal structure of TM1643==
-|PDB= 1h2h |SIZE=350|CAPTION= <scene name='initialview01'>1h2h</scene>, resolution 2.6&Aring;
+<StructureSection load='1h2h' size='340' side='right'caption='[[1h2h]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-|SITE= <scene name='pdbsite=NAD:Nad+Binding+Site+For+Chain+A'>NAD</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
+<table><tr><td colspan='2'>[[1h2h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H2H FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01958 DUF108], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG1712 COG1712], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03447 NAD_binding_3]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h2h OCA], [https://pdbe.org/1h2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h2h RCSB], [https://www.ebi.ac.uk/pdbsum/1h2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h2h ProSAT], [https://www.topsan.org/Proteins/NESGC/1h2h TOPSAN]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1h2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h2h OCA], [http://www.ebi.ac.uk/pdbsum/1h2h PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1h2h RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/ASPD_THEMA ASPD_THEMA] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate. Does not show aspartate oxidase activity. Is also able to catalyze the reverse reaction, i.e. the reductive amination of oxaloacetate.<ref>PMID:12496312</ref>
+== Evolutionary Conservation ==
-'''CRYSTAL STRUCTURE OF TM1643'''
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
-==Overview==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h2/1h2h_consurf.spt"</scriptWhenChecked>
-The open reading frame TM1643 of Thermotoga maritima belongs to a large family of proteins, with homologues in bacteria, archaea, and eukaryotes. TM1643 is found in an operon with two other genes that encode enzymes involved in the biosynthesis of NAD. In several bacteria, the gene in the position occupied by TM1643 encodes an aspartate oxidase (NadB), which synthesizes iminoaspartate as a substrate for NadA, the next enzyme in the pathway. The amino acid sequence of TM1643 does not share any recognizable homology with aspartate oxidase or with other proteins of known functions or structures. To help define the biological functions of TM1643, we determined its crystal structure at 2.6A resolution and performed a series of screens for enzymatic function. The structure reveals the presence of an N-terminal Rossmann fold domain with a bound NAD(+) cofactor and a C-terminal alpha+beta domain. The structural information suggests that TM1643 may be a dehydrogenase and the active site of the enzyme is located at the interface between the two domains. The enzymatic characterization of TM1643 revealed that it possesses NAD or NADP-dependent dehydrogenase activity toward l-aspartate but no aspartate oxidase activity. The product of the aspartate dehydrogenase activity is also iminoaspartate. Therefore, our studies demonstrate that two different enzymes, an oxidase and a dehydrogenase, may have evolved to catalyze the first step of NAD biosynthesis in prokaryotes. TM1643 establishes a new class of amino acid dehydrogenases.
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==About this Structure==
+  </jmolCheckbox>
-H2H is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1H2H OCA].
+</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=1h2h ConSurf].
+<div style="clear:both"></div>
-==Reference==
+== References ==
-Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643., Yang Z, Savchenko A, Yakunin A, Zhang R, Edwards A, Arrowsmith C, Tong L, J Biol Chem. 2003 Mar 7;278(10):8804-8. Epub 2002 Dec 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12496312 12496312]
+<references/>
-[[Category: Single protein]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: Arrowsmith, C.]]
+[[Category: Arrowsmith C]]
-[[Category: Edwards, A.]]
+[[Category: Edwards A]]
-[[Category: NESG, Northeast Structural Genomics Consortium.]]
+[[Category: Savchenko A]]
-[[Category: Savchenko, A.]]
+[[Category: Tong L]]
-[[Category: Tong, L.]]
+[[Category: Yang Z]]
-[[Category: Yang, Z.]]
-[[Category: possible nad-dependent oxidoreductase,structural genomic]]
-[[Category: psi,protein structure initiative,nesg,northeast structural genomics consortium]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:56:19 2008''

1h2h

From Proteopedia

Current revision

Crystal structure of TM1643

Structural highlights

Function

Evolutionary Conservation

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox