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[[Image:1lrw.gif|left|200px]]


{{Structure
==Crystal structure of methanol dehydrogenase from P. denitrificans==
|PDB= 1lrw |SIZE=350|CAPTION= <scene name='initialview01'>1lrw</scene>, resolution 2.50&Aring;
<StructureSection load='1lrw' size='340' side='right'caption='[[1lrw]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=PQQ:PYRROLOQUINOLINE QUINONE'>PQQ</scene>
<table><tr><td colspan='2'>[[1lrw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LRW FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
|GENE=  
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PQQ:PYRROLOQUINOLINE+QUINONE'>PQQ</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1lrw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lrw OCA], [https://pdbe.org/1lrw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lrw RCSB], [https://www.ebi.ac.uk/pdbsum/1lrw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lrw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DHM2_PARDE DHM2_PARDE] Catalyzes the oxidation of primary alcohols including methanol (By similarity).
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/1lrw_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1lrw ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


'''Crystal structure of methanol dehydrogenase from P. denitrificans'''
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<ref>PMID:14505072</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1lrw" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
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.
*[[Methanol dehydrogenase|Methanol dehydrogenase]]
 
== References ==
==About this Structure==
<references/>
1LRW is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LRW OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
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:[http://www.ncbi.nlm.nih.gov/pubmed/14505072 14505072]
[[Category: Alcohol dehydrogenase (acceptor)]]
[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
[[Category: Protein complex]]
[[Category: Dai W-W]]
[[Category: Dai, W W.]]
[[Category: Davidson VL]]
[[Category: Davidson, V L.]]
[[Category: He Y-N]]
[[Category: He, Y N.]]
[[Category: Mathews FS]]
[[Category: Mathews, F S.]]
[[Category: White SA]]
[[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://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:34:30 2008''

Latest revision as of 03:13, 21 November 2024

Crystal structure of methanol dehydrogenase from P. denitrificansCrystal structure of methanol dehydrogenase from P. denitrificans

Structural highlights

1lrw is a 4 chain structure with sequence from Paracoccus denitrificans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DHM2_PARDE Catalyzes the oxidation of primary alcohols including methanol (By similarity).

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 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.

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[1]

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

See Also

References

  1. ↑ Xia ZX, Dai WW, He YN, White SA, Mathews FS, Davidson VL. X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i. J Biol Inorg Chem. 2003 Nov;8(8):843-54. Epub 2003 Sep 23. PMID:14505072 doi:10.1007/s00775-003-0485-0

1lrw, resolution 2.50Å

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