1omo

From Proteopedia

(Difference between revisions)

Revision as of 00:59, 10 September 2015

alanine dehydrogenase dimer w/bound NAD (archaeal)

Structural highlights

1omo is a 2 chain structure with sequence from Arcfl. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Activity:	Alanine dehydrogenase, with EC number 1.4.1.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[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]^[1]

Evolutionary Conservation

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

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Schroder I, Vadas A, Johnson E, Lim S, Monbouquette HG. A novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu-crystallin. J Bacteriol. 2004 Nov;186(22):7680-9. PMID:15516582 doi:http://dx.doi.org/10.1128/JB.186.22.7680-7689.2004
↑ Gallagher DT, Monbouquette HG, Schroder I, Robinson H, Holden MJ, Smith NN. Structure of alanine dehydrogenase from Archaeoglobus: active site analysis and relation to bacterial cyclodeaminases and mammalian mu crystallin. J Mol Biol. 2004 Sep 3;342(1):119-30. PMID:15313611 doi:10.1016/j.jmb.2004.06.090

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 2: / Line 2: @@
 <StructureSection load='1omo' size='340' side='right' caption='[[1omo]], [[Resolution|resolution]] 2.32&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1omo]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OMO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1omo]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OMO FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1omo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1omo RCSB], [http://www.ebi.ac.uk/pdbsum/1omo PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1omo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omo OCA], [http://pdbe.org/1omo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1omo RCSB], [http://www.ebi.ac.uk/pdbsum/1omo PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/O28608_ARCFU O28608_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.<ref>PMID:15516582</ref>
+[[http://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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 27: / Line 27: @@
 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/>
@@ Line 32: / Line 33: @@
 </StructureSection>
 [[Category: Alanine dehydrogenase]]
-[[Category: Archaeoglobus fulgidus]]
+[[Category: Arcfl]]
 [[Category: Gallagher, D T]]
 [[Category: Holden, M J]]

1omo

From Proteopedia

Revision as of 00:59, 10 September 2015

alanine dehydrogenase dimer w/bound NAD (archaeal)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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