1lrw: Difference between revisions

Revision as of 14:47, 21 February 2008

Crystal structure of methanol dehydrogenase from P. denitrificans

OverviewOverview

The X-ray structure of methanol dehydrogenase (MEDH) from Paracoccus denitrificans (MEDH-PD) was determined at 2.5 A resolution using molecular replacement based on the structure of MEDH from Methylophilus methylotrophus W3A1 (MEDH-WA). The overall structures from the two bacteria are similar to each other except that the former has a longer C-terminal tail in each subunit and shows local differences in several insertion regions. The "X-ray sequence" of the segment alphaGly444-alphaLeu452 was established, including one insertion and seven replacements compared with the reported sequence. The primary electron acceptor of MEDH-PD is cytochrome c-551i (Cyt c551i). Based on the crystal structure of MEDH-PD and of the published structure of Cyt c551i, their interactions were investigated by molecular modeling. As a guide and starting point, the covalently attached cytochrome and PQQ domains of the alcohol dehydrogenase from Pseudomonas putida HK5 (ADH2B) were used. In the modeling, two molecules of Cyt c551i could be accommodated in their interaction with the MEDH heterotetramer in accordance with the two-fold molecular symmetry of the latter. Two models are proposed, in both of which electrostatic and hydrogen bonding interactions make major contributions to inter-protein binding. One of these models involves salt bridges from alphaArg99 of MEDH to the heme propionic acids of Cyt c551i and the other involves salt bridges from alphaArg426 of MEDH to Glu112 of Cyt c551i. Both involve salt bridges from alphaLys93 of MEDH to Asp75 of Cyt c551i. The size and nature of the cytochrome/quinoprotein heterodimer interfaces and calculations of electronic coupling and electron transfer rates favor one of these models over the other.

About this StructureAbout this Structure

1LRW is a Protein complex structure of sequences from Paracoccus denitrificans with and as ligands. Active as Alcohol dehydrogenase (acceptor), with EC number 1.1.99.8 Full crystallographic information is available from OCA.

ReferenceReference

X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i., Xia ZX, Dai WW, He YN, White SA, Mathews FS, Davidson VL, J Biol Inorg Chem. 2003 Nov;8(8):843-54. Epub 2003 Sep 23. PMID:14505072

Page seeded by OCA on Thu Feb 21 13:47:47 2008

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-[[Image:1lrw.gif|left|200px]]<br /><applet load="1lrw" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1lrw.gif|left|200px]]<br /><applet load="1lrw" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1lrw, resolution 2.50&Aring;" />
 '''Crystal structure of methanol dehydrogenase from P. denitrificans'''<br />
 ==Overview==
-The X-ray structure of methanol dehydrogenase (MEDH) from Paracoccus, denitrificans (MEDH-PD) was determined at 2.5 A resolution using molecular, replacement based on the structure of MEDH from Methylophilus, methylotrophus W3A1 (MEDH-WA). The overall structures from the two, bacteria are similar to each other except that the former has a longer, C-terminal tail in each subunit and shows local differences in several, insertion regions. The "X-ray sequence" of the segment, alphaGly444-alphaLeu452 was established, including one insertion and seven, replacements compared with the reported sequence. The primary electron, acceptor of MEDH-PD is cytochrome c-551i (Cyt c551i). Based on the crystal, structure of MEDH-PD and of the published structure of Cyt c551i, their, interactions were investigated by molecular modeling. As a guide and, starting point, the covalently attached cytochrome and PQQ domains of the, alcohol dehydrogenase from Pseudomonas putida HK5 (ADH2B) were used. In, the modeling, two molecules of Cyt c551i could be accommodated in their, interaction with the MEDH heterotetramer in accordance with the two-fold, molecular symmetry of the latter. Two models are proposed, in both of, which electrostatic and hydrogen bonding interactions make major, contributions to inter-protein binding. One of these models involves salt, bridges from alphaArg99 of MEDH to the heme propionic acids of Cyt c551i, and the other involves salt bridges from alphaArg426 of MEDH to Glu112 of, Cyt c551i. Both involve salt bridges from alphaLys93 of MEDH to Asp75 of, Cyt c551i. The size and nature of the cytochrome/quinoprotein heterodimer, interfaces and calculations of electronic coupling and electron transfer, rates favor one of these models over the other.
+The X-ray structure of methanol dehydrogenase (MEDH) from Paracoccus denitrificans (MEDH-PD) was determined at 2.5 A resolution using molecular replacement based on the structure of MEDH from Methylophilus methylotrophus W3A1 (MEDH-WA). The overall structures from the two bacteria are similar to each other except that the former has a longer C-terminal tail in each subunit and shows local differences in several insertion regions. The "X-ray sequence" of the segment alphaGly444-alphaLeu452 was established, including one insertion and seven replacements compared with the reported sequence. The primary electron acceptor of MEDH-PD is cytochrome c-551i (Cyt c551i). Based on the crystal structure of MEDH-PD and of the published structure of Cyt c551i, their interactions were investigated by molecular modeling. As a guide and starting point, the covalently attached cytochrome and PQQ domains of the alcohol dehydrogenase from Pseudomonas putida HK5 (ADH2B) were used. In the modeling, two molecules of Cyt c551i could be accommodated in their interaction with the MEDH heterotetramer in accordance with the two-fold molecular symmetry of the latter. Two models are proposed, in both of which electrostatic and hydrogen bonding interactions make major contributions to inter-protein binding. One of these models involves salt bridges from alphaArg99 of MEDH to the heme propionic acids of Cyt c551i and the other involves salt bridges from alphaArg426 of MEDH to Glu112 of Cyt c551i. Both involve salt bridges from alphaLys93 of MEDH to Asp75 of Cyt c551i. The size and nature of the cytochrome/quinoprotein heterodimer interfaces and calculations of electronic coupling and electron transfer rates favor one of these models over the other.
 ==About this Structure==
-LRW is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans] with CA and PQQ as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(acceptor) Alcohol dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.8 1.1.99.8] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LRW OCA].
+LRW is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=PQQ:'>PQQ</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Alcohol_dehydrogenase_(acceptor) Alcohol dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.99.8 1.1.99.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRW OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Paracoccus denitrificans]]
 [[Category: Protein complex]]
-[[Category: Dai, W.W.]]
+[[Category: Dai, W W.]]
-[[Category: Davidson, V.L.]]
+[[Category: Davidson, V L.]]
-[[Category: He, Y.N.]]
+[[Category: He, Y N.]]
-[[Category: Mathews, F.S.]]
+[[Category: Mathews, F S.]]
-[[Category: White, S.A.]]
+[[Category: White, S A.]]
-[[Category: Xia, Z.X.]]
+[[Category: Xia, Z X.]]
 [[Category: CA]]
 [[Category: PQQ]]
 [[Category: heavy subunits: 8-fold beta-propeller superbarrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:49:24 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:47:47 2008''