1yiq

From Proteopedia

(Difference between revisions)

Revision as of 02:32, 12 September 2015

Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADHIIG from Pseudomonas putida HK5. Compariison to the other quinohemoprotein alcohol dehydrogenase ADHIIB found in the same microorganism.

Structural highlights

1yiq is a 1 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Related:	1kv9
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[QGDA_PSEPU] Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Active with primary alcohols, glycerol, 1,2-propanediol, 1,3-propanediol but not with methanol or sugar alcohols such as D-sorbitol.^[1] ^[2] ^[3]

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

Depending on the alcohols used as growth substrates, Pseudomonas putida HK5 produces two distinct quinohemoprotein alcohol dehydrogenases, ADH-IIB and ADH-IIG, both of which contain pyrroloquinoline quinone (PQQ) and heme c as the prosthetic groups but show different substrate specificities, especially for diol substrates. Molecular cloning of the gene of ADH-IIB and its crystal structure are already reported. Here, molecular cloning of the gene, qgdA, and solution of the three-dimensional structure of ADH-IIG are reported. The enzyme consists of 718 amino acid residues including a signal sequence of 29 amino acid residues. The PQQ domain is highly homologous to other quinoproteins, especially to quinohemoproteins. The crystal structure of ADH-IIG, determined at 2.2A resolution, shows that the overall structure and the amino acid residues involved in PQQ binding are quite similar to ADH-IIB and to another quinohemoprotein ADH, qhEDH from Comamonas testosteroni. However, the lengths of the linker regions connecting the PQQ and the cytochrome domains are different from each other, leading to a significant difference in orientation of the cytochrome domain with respect to the PQQ domain. Apart from ADH-IIB and qhEDH, ADH-IIG has an extra 12-residue helix within loop 3 in the PQQ domain and an extra 3(10) helix in the C terminus of the cytochrome domain, and both helices appear parallel and linked by a hydrogen bond. The amino acid residues contacting substrate/product in the crystal structures are also different among them. In the crystal structure of ADH-IIG with 1,2-propanediol, one of the hydroxyl groups of the substrate forms a hydrogen bond with O5 of PQQ and OD1 of Asp300, and the other interacts with a water molecule and with NE2 of Trp386, the corresponding residue of which is not found in ADH-IIB and qhEDH, and might be the residue responsible for making ADH-IIG prefer diol substrates.

Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5.,Toyama H, Chen ZW, Fukumoto M, Adachi O, Matsushita K, Mathews FS J Mol Biol. 2005 Sep 9;352(1):91-104. PMID:16061256^[4]

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

References

↑ Promden W, Vangnai AS, Pongsawasdi P, Adachi O, Matsushita K, Toyama H. Disruption of quinoprotein ethanol dehydrogenase gene and adjacent genes in Pseudomonas putida HK5. FEMS Microbiol Lett. 2008 Mar;280(2):203-9. doi:, 10.1111/j.1574-6968.2008.01060.x. Epub 2008 Jan 19. PMID:18218017 doi:http://dx.doi.org/10.1111/j.1574-6968.2008.01060.x
↑ Promden W, Vangnai AS, Toyama H, Matsushita K, Pongsawasdi P. Analysis of the promoter activities of the genes encoding three quinoprotein alcohol dehydrogenases in Pseudomonas putida HK5. Microbiology. 2009 Feb;155(Pt 2):594-603. doi: 10.1099/mic.0.021956-0. PMID:19202108 doi:http://dx.doi.org/10.1099/mic.0.021956-0
↑ Toyama H, Fujii A, Matsushita K, Shinagawa E, Ameyama M, Adachi O. Three distinct quinoprotein alcohol dehydrogenases are expressed when Pseudomonas putida is grown on different alcohols. J Bacteriol. 1995 May;177(9):2442-50. PMID:7730276
↑ Toyama H, Chen ZW, Fukumoto M, Adachi O, Matsushita K, Mathews FS. Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5. J Mol Biol. 2005 Sep 9;352(1):91-104. PMID:16061256 doi:10.1016/j.jmb.2005.06.078

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 5: / Line 5: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</scene>, <scene name='pdbligand=PQQ:PYRROLOQUINOLINE+QUINONE'>PQQ</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kv9|1kv9]]</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=1yiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yiq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yiq RCSB], [http://www.ebi.ac.uk/pdbsum/1yiq 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=1yiq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yiq OCA], [http://pdbe.org/1yiq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yiq RCSB], [http://www.ebi.ac.uk/pdbsum/1yiq PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q4W6G0_PSEPU Q4W6G0_PSEPU]] Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Active with primary alcohols, glycerol, 1,2-propanediol, 1,3-propanediol but not with methanol or sugar alcohols such as D-sorbitol.<ref>PMID:7730276</ref> <ref>PMID:18218017</ref> <ref>PMID:19202108</ref>
+[[http://www.uniprot.org/uniprot/QGDA_PSEPU QGDA_PSEPU]] Catalyzes the dye-linked oxidation of primary alcohols to the corresponding aldehydes and the (subsequent) oxidation of the aldehydes to carboxylic acids. Active with primary alcohols, glycerol, 1,2-propanediol, 1,3-propanediol but not with methanol or sugar alcohols such as D-sorbitol.<ref>PMID:18218017</ref> <ref>PMID:19202108</ref> <ref>PMID:7730276</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 1yiq" style="background-color:#fffaf0;"></div>
 ==See Also==

1yiq

From Proteopedia

Revision as of 02:32, 12 September 2015

Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADHIIG from Pseudomonas putida HK5. Compariison to the other quinohemoprotein alcohol dehydrogenase ADHIIB found in the same microorganism.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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