Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2008) Nucleic Acids Res , doi:10.1093/nar/gkn808

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PQQ beta-propeller repeat

There are 7052 PQQ domains in 1378 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a PQQ domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with PQQ domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Xia Z, Dai W, Zhang Y, White SA, Boyd GD, Mathews FS
  • Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1.
  • J Mol Biol. 1996; 259: 480-501
  • Display abstract

  • The DNA sequences for the genes encoding the heavy and light subunits of methanol dehydrogenase from Methylophilus methylotrophus W3A1 have been determined. The deduced amino acid sequence has enabled the structure of the enzyme to be refined at 2.4 angstrom resolution against X-ray data collected on a Hamlin area detector. The structure was refined using the programs PROFFT and X-PLOR with several model building step interspersed. The final model contains two heavy chains (571 amino acids), two light chains (69 amino acids), two molecules of pyrroloquinoline quinone, two Ca2+ and 521 solvent molecules. Each half molecule contains four disulfide linkages and four cis peptides. One of the disulfides is formed from two adjacent cysteine residues linked by a trans peptide which creates a novel eight-membered ring. The heavy subunit is an 8-fold beta-propeller, each "blade" of which is a four-stranded antiparallel twisted beta-sheet. The light chain is an elongated subunit stretching across the surface of the heavy subunit, with residues 1 to 32 containing four beta-turns and residues 33 to 62 forming a helix; however, it neither interacts with the active site, nor the other HL dimer and its functional role is obscure. Around the 8-fold beta-propeller there is a repeating pattern of tryptophan residues located in the outer strand of seven of the eight beta-leaflets, each packed between adjacent leaflets. Each of these tryptophan residues is centered in the beta-strand and participates in the main chain hydrogen bonding of the sheet. Five of the seven tryptophan residues have closely similar interactions with the adjacent beta-leaflet including stacking of the tryptophan indole rings against a peptide plane and formation of a hydrogen bond from NE1 of the indole ring to a main-chain carbonyl. This repeating pattern is conserved over a number of MEDH sequences. The PQQ is located on the pseudo 8-fold rotation axis of the heavy subunit, in a funnel-shaped internal cavity, sandwiched between the indole ring of Trp237 and the two sulfur atoms of the Cys103-Cys104 vicinal disulfide. A hexacoordinate Ca2+ is bound in the active site by one nitrogen and five oxygen ligands, three from the PQQ and the others from two protein side-chains. In the active site an isolated solvent molecule is bound to the O5 of PQQ and to a nearby aspartate side-chain; its position may be the binding site for methanol. The aspartate might than serve as a general base for proton abstraction from the substrate hydroxyl. The C5 atom of PQQ could be activated by electrophilic catalysis by a nearby argenine side-chain or by the calcium ion bound to PQQ.

  • Blake CC, Ghosh M, Harlos K, Avezoux A, Anthony C
  • The active site of methanol dehydrogenase contains a disulphide bridge between adjacent cysteine residues.
  • Nat Struct Biol. 1994; 1: 102-5
  • Display abstract

  • Adjacent cysteine residues can only form disulphide bridges in a distorted structure containing a cis-peptide link. Such bridges are extremely uncommon, identified so far in the acetyl choline receptor alone where the structure of the bridge is undetermined. Here we present the first molecular description of a disulphide bridge of this type in the quinoprotein methanol dehydrogenase from Methylobacterium extorquens. We show that this structure occurs in close proximity to the pyrrolo-quinoline quinone prosthetic group and a calcium ion in the active site of the enzyme. This unusual disulphide bridge appears to play a role in the electron transfer reaction mediated by methanol dehydrogenase.

  • Duine JA, Jongejan JA
  • Quinoproteins, enzymes with pyrrolo-quinoline quinone as cofactor.
  • Annu Rev Biochem. 1989; 58: 403-26
• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 19.73 map00030 Pentose phosphate pathway 13.87 map00680 Methane metabolism 13.87 map00010 Glycolysis / Gluconeogenesis 13.87 map00631 1,2-Dichloroethane degradation 13.87 map00650 Butanoate metabolism 13.87 map00640 Propanoate metabolism 2.13 map00440 Aminophosphonate metabolism 2.13 map00903 Limonene and pinene degradation 2.13 map00362 Benzoate degradation via hydroxylation 1.07 map00562 Inositol phosphate metabolism 1.07 map00632 Benzoate degradation via CoA ligation 1.07 map00400 Phenylalanine, tyrosine and tryptophan biosynthesis 0.53 map03090 Type II secretion system 0.27 map00300 Lysine biosynthesis 0.27 map00860 Porphyrin and chlorophyll metabolism 0.27 map00310 Lysine degradation This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with PQQ domain which could be assigned to a KEGG orthologous group, and not all proteins containing PQQ domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of PQQ domains in PDB

  PDB code	Main view	Title
  1flg		Crystal structure of the quinoprotein ethanol dehydrogenase from pseudomonas aeruginosa
  1g72		Catalytic mechanism of quinoprotein methanol dehydrogenase: a theoretical and x-ray crystallographic investigation
  1h4i		Methylobacterium extorquens methanol dehydrogenase
  1h4j		Methylobacterium extorquens methanol dehydrogenase d303e mutant
  1kb0		Crystal structure of quinohemoprotein alcohol dehydrogenase from comamonas testosteroni
  1kv9		Structure at 1.9 a resolution of a quinohemoprotein alcohol dehydrogenase from pseudomonas putida hk5
  1lrw		Crystal structure of methanol dehydrogenase from p. denitrificans
  1w6s		The high resolution structure of methanol dehydrogenase from methylobacterium extorquens
  1yiq		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.
  2ad6		Crystal structure of methanol dehydrogenase from m. w3a1 (form c)
  2ad7		Crystal structure of methanol dehydrogenase from m. w3a1 (form c) in the presence of methanol
  2ad8		Crystal structure of methanol dehydrogenase from m. w3a1 (form c) in the presence of ethanol
  2be1		Structure of the compact lumenal domain of yeast ire1
  2d0v		Crystal structure of methanol dehydrogenase from hyphomicrobium denitrificans
  2hz6		The crystal structure of human ire1-alpha luminal domain
  3hxj
  4aah		Methanol dehydrogenase from methylophilus w3a1

• Links (links to other resources describing this domain)

• INTERPRO	IPR002372