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600 a.a.
83 a.a.
_CA
 A primary alcohol |
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acceptor |
= |
 an aldehyde |
+ |
reduced acceptor |
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Bound ligand (Het Group name = PQQ) corresponds exactly |
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Key reference
DOI no: 10.1007/s00775-003-0485-0 J Biol Inorg Chem 8:843-854 (2003) PubMed id: 14505072
X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i. Z.X.Xia, W.W.Dai, Y.N.He, S.A.White, F.S.Mathews, V.L.Davidson. ABSTRACT
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.
Literature references that cite this PDB file's key reference
PubMed id Reference
19224199 B.Mennenga, C.W.Kay, and H.Görisch (2009).
Quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: the unusual disulfide ring formed by adjacent cysteine residues is essential for efficient electron transfer to cytochrome c550.Arch Microbiol, 191, 361-367.
15716266 V.Y.Kuznetsov, E.Blair, P.J.Farmer, T.L.Poulos, A.Pifferitti, and I.F.Sevrioukova (2005).
The putidaredoxin reductase-putidaredoxin electron transfer complex: theoretical and experimental studies.J Biol Chem, 280, 16135-16142.
15273299 S.Y.Reddy, and T.C.Bruice (2004).
Determination of enzyme mechanisms by molecular dynamics: studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase.Protein Sci, 13, 1965-1978. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.
