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PDBsum entry 1g72

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1g72
Jmol PyMol
Contents
Protein chains
571 a.a. *
57 a.a. *
Ligands
PQQ ×2
Metals
_CA ×2
Waters ×614
* Residue conservation analysis
PDB id:
1g72
Name: Oxidoreductase
Title: Catalytic mechanism of quinoprotein methanol dehydrogenase: theoretical and x-ray crystallographic investigation
Structure: Methanol dehydrogenase heavy subunit. Chain: a, c. Synonym: mdh large alpha subunit. Methanol dehydrogenase light subunit. Chain: b, d. Synonym: mdh small alpha subunit. Ec: 1.1.99.8
Source: Methylophilus methylotrophus. Organism_taxid: 2327. Strain: w3a1. Strain: w3a1
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.161     R-free:   0.190
Authors: Y.Zheng,Z.Xia,Z.Chen,T.C.Bruice,F.S.Mathews
Key ref:
Y.J.Zheng et al. (2001). Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation. Proc Natl Acad Sci U S A, 98, 432-434. PubMed id: 11149955 DOI: 10.1073/pnas.021547498
Date:
08-Nov-00     Release date:   24-Jan-01    
Supersedes: 1b2n
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P38539  (DHM1_METME) -  Methanol dehydrogenase [cytochrome c] subunit 1
Seq:
Struc:
 
Seq:
Struc:
573 a.a.
571 a.a.
Protein chains
Pfam   ArchSchema ?
P38540  (DHM2_METME) -  Methanol dehydrogenase [cytochrome c] subunit 2
Seq:
Struc:
91 a.a.
57 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.1.1.2.7  - Methanol dehydrogenase (cytochrome c).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L) + 2 H(+)
primary alcohol
+ 2 × cytochrome c(L)
= aldehyde
+ 2 × reduced cytochrome c(L)
+ 2 × H(+)
      Cofactor: Pyrroloquinoline quinone
Pyrroloquinoline quinone
Bound ligand (Het Group name = PQQ) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     methanol ferricytochrome-c oxidoreductase activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.021547498 Proc Natl Acad Sci U S A 98:432-434 (2001)
PubMed id: 11149955  
 
 
Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation.
Y.J.Zheng, Xia Zx, Chen Zw, F.S.Mathews, T.C.Bruice.
 
  ABSTRACT  
 
The catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (MDH) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (PQQ). A crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. A theoretical analysis and an improved refinement of the 1.9-A resolution crystal structure of MDH from Methylophilus methylotrophus W3A1 in the presence of methanol, reported earlier, indicates that the observed tetrahedral configuration of the C-5 atom of PQQ in that study represents the C-5-reduced form of the cofactor and lends support for a hydride transfer mechanism for MDH.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. (A) Chemical structure of PQQ with the numbering of the ring atoms indicated. (B) Addition-elimination mechanism for oxidation of methanol by PQQ in methanol dehydrogenase involving base catalysis by Asp297. (C) Hydride transfer mechanism for methanol oxidation involving a C-5-reduced intermediate of PQQ and base catalysis by Asp297.
Figure 3.
Fig. 3. Environment of the water molecule hydrogen bonded to Asp297 and C-5 of PQQ. Electrostatic and hydrogen bonding interactions are indicated by dotted lines, and van der Waals interactions by dashed lines with distances in Å. This diagram was prepared by using the program MOLSCRIPT (23).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21356200 J.Li, J.H.Gan, F.S.Mathews, and Z.X.Xia (2011).
The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase.
  Biochem Biophys Res Commun, 406, 621-626.
PDB codes: 2ad6 2ad7 2ad8
20059399 L.M.Blank, B.E.Ebert, K.Buehler, and B.Bühler (2010).
Redox biocatalysis and metabolism: molecular mechanisms and metabolic network analysis.
  Antioxid Redox Signal, 13, 349-394.  
17215371 X.Zhang, S.Y.Reddy, and T.C.Bruice (2007).
Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase.
  Proc Natl Acad Sci U S A, 104, 745-749.  
16567634 C.W.Kay, B.Mennenga, H.Görisch, and R.Bittl (2006).
Substrate binding in quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa studied by electron-nuclear double resonance.
  Proc Natl Acad Sci U S A, 103, 5267-5272.  
14997549 I.Hudáky, Z.Gáspári, O.Carugo, M.Cemazar, S.Pongor, and A.Perczel (2004).
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations.
  Proteins, 55, 152-168.  
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.  
15520392 S.Y.Reddy, and T.C.Bruice (2004).
Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: a computational approach.
  Proc Natl Acad Sci U S A, 101, 15887-15892.  
12383230 Y.Zhang, and P.A.Rosenberg (2002).
The essential nutrient pyrroloquinoline quinone may act as a neuroprotectant by suppressing peroxynitrite formation.
  Eur J Neurosci, 16, 1015-1024.  
12057198 Z.W.Chen, K.Matsushita, T.Yamashita, T.A.Fujii, H.Toyama, O.Adachi, H.D.Bellamy, and F.S.Mathews (2002).
Structure at 1.9 A resolution of a quinohemoprotein alcohol dehydrogenase from Pseudomonas putida HK5.
  Structure, 10, 837-849.
PDB code: 1kv9
12116408 A.Jongejan, J.A.Jongejan, and W.R.Hagen (2001).
Direct hydride transfer in the reaction mechanism of quinoprotein alcohol dehydrogenases: a quantum mechanical investigation.
  J Comput Chem, 22, 1732-1749.  
11679760 A.Oubrie, E.G.Huizinga, H.J.Rozeboom, K.H.Kalk, G.A.de Jong, J.A.Duine, and B.W.Dijkstra (2001).
Crystallization of quinohaemoprotein alcohol dehydrogenase from Comamonas testosteroni: crystals with unique optical properties.
  Acta Crystallogr D Biol Crystallogr, 57, 1732-1734.  
11761326 C.Anthony (2001).
Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes.
  Antioxid Redox Signal, 3, 757-774.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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