1omo

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[[Image:1omo.gif|left|200px]]<br /><applet load="1omo" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1omo, resolution 2.32&Aring;" />
 
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'''alanine dehydrogenase dimer w/bound NAD (archaeal)'''<br />
 
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==Overview==
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==alanine dehydrogenase dimer w/bound NAD (archaeal)==
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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.
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<StructureSection load='1omo' size='340' side='right'caption='[[1omo]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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1OMO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus] with <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alanine_dehydrogenase Alanine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.1 1.4.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMO OCA].
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</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>
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<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>
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==Reference==
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<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>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15313611 15313611]
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</table>
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[[Category: Alanine dehydrogenase]]
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/om/1omo_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Gallagher, D T.]]
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[[Category: Gallagher DT]]
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[[Category: Holden, M J.]]
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[[Category: Holden MJ]]
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[[Category: Monbouquette, H G.]]
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[[Category: Monbouquette HG]]
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[[Category: Schroeder, I.]]
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[[Category: Schroeder I]]
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[[Category: Smith, N N.]]
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[[Category: Smith NN]]
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[[Category: NA]]
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[[Category: NAD]]
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[[Category: beta-sandwich-dimer]]
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[[Category: human mu crystallin homolog]]
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[[Category: human thyroid-hormone-binder homolog]]
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[[Category: rossmann-fold nad domain]]
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[[Category: two-domain]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:19:30 2008''
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Current revision

alanine dehydrogenase dimer w/bound NAD (archaeal)

PDB ID 1omo

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