1omo: Difference between revisions

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<StructureSection load='1omo' size='340' side='right'caption='[[1omo]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
<StructureSection load='1omo' size='340' side='right'caption='[[1omo]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1omo]] 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=1OMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OMO FirstGlance]. <br>
<table><tr><td colspan='2'>[[1omo]] 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=1OMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OMO 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=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]] 2.32&#8491;</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alanine_dehydrogenase Alanine dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.1 1.4.1.1] </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=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=1omo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omo OCA], [https://pdbe.org/1omo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1omo RCSB], [https://www.ebi.ac.uk/pdbsum/1omo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1omo 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=1omo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omo OCA], [https://pdbe.org/1omo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1omo RCSB], [https://www.ebi.ac.uk/pdbsum/1omo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1omo ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/ALADH_ARCFU ALADH_ARCFU]] Catalyzes the NAD(+)-dependent oxidative deamination of L-alanine to pyruvate, and the reverse reaction, the reductive amination of pyruvate. Its physiological role is not known. Can not use NADP(+) instead of NAD(+) as a cosubstrate. In the deamination direction, can also efficiently use L-2-aminobutyrate as substrate. In the reductive amination direction, also exhibits high activity with 2-oxobutyrate and oxaloacetate as substrate. In contrast to bacterial homologs, does not exhibit any ornithine cyclodeaminase activity.[HAMAP-Rule:MF_00935]<ref>PMID:15516582</ref>
[https://www.uniprot.org/uniprot/ALADH_ARCFU ALADH_ARCFU] Catalyzes the NAD(+)-dependent oxidative deamination of L-alanine to pyruvate, and the reverse reaction, the reductive amination of pyruvate. Its physiological role is not known. Can not use NADP(+) instead of NAD(+) as a cosubstrate. In the deamination direction, can also efficiently use L-2-aminobutyrate as substrate. In the reductive amination direction, also exhibits high activity with 2-oxobutyrate and oxaloacetate as substrate. In contrast to bacterial homologs, does not exhibit any ornithine cyclodeaminase activity.[HAMAP-Rule:MF_00935]<ref>PMID:15516582</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=1omo 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=1omo ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The hyperthermophilic archaeon Archaeoglobus fulgidus contains an L-Ala dehydrogenase (AlaDH, EC 1.4.1.1) that is not homologous to known bacterial dehydrogenases and appears to represent a previously unrecognized archaeal group of NAD-dependent dehydrogenases. The gene (Genbank; TIGR AF1665) was annotated initially as an ornithine cyclodeaminase (OCD) on the basis of strong homology with the mu crystallin/OCD protein family. We report the structure of the NAD-bound AF1665 AlaDH (AF-AlaDH) at 2.3 A in a C2 crystal form with the 70 kDa dimer in the asymmetric unit, as the first structural representative of this family. Consistent with its lack of homology to bacterial AlaDH proteins, which are mostly hexameric, the archaeal dimer has a novel structure. Although both types of AlaDH enzyme include a Rossmann-type NAD-binding domain, the arrangement of strands in the C-terminal half of this domain is novel, and the other (catalytic) domain in the archaeal protein has a new fold. The active site presents a cluster of conserved Arg and Lys side-chains over the pro-R face of the cofactor. In addition, the best ordered of the 338 water molecules in the structure is positioned well for mechanistic interaction. The overall structure and active site are compared with other dehydrogenases, including the AlaDH from Phormidium lapideum. Implications for the catalytic mechanism and for the structures of homologs are considered. The archaeal AlaDH represents an ancient and previously undescribed subclass of Rossmann-fold proteins that includes bacterial ornithine and lysine cyclodeaminases, marsupial lens proteins and, in man, a thyroid hormone-binding protein that exhibits 30% sequence identity with AF1665.
Structure of alanine dehydrogenase from Archaeoglobus: active site analysis and relation to bacterial cyclodeaminases and mammalian mu crystallin.,Gallagher DT, Monbouquette HG, Schroder I, Robinson H, Holden MJ, Smith NN J Mol Biol. 2004 Sep 3;342(1):119-30. PMID:15313611<ref>PMID:15313611</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1omo" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Alanine dehydrogenase]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Arcfl]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Gallagher, D T]]
[[Category: Gallagher DT]]
[[Category: Holden, M J]]
[[Category: Holden MJ]]
[[Category: Monbouquette, H G]]
[[Category: Monbouquette HG]]
[[Category: Schroeder, I]]
[[Category: Schroeder I]]
[[Category: Smith, N N]]
[[Category: Smith NN]]
[[Category: Beta-sandwich-dimer]]
[[Category: Human mu crystallin homolog]]
[[Category: Human thyroid-hormone-binder homolog]]
[[Category: Oxidoreductase]]
[[Category: Rossmann-fold nad domain]]
[[Category: Two-domain]]

Latest revision as of 08:01, 14 February 2024

alanine dehydrogenase dimer w/bound NAD (archaeal)

1omo, resolution 2.32Å

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