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PDBsum entry 1dii
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
1dii

 

 

 

 

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Contents
Protein chains
515 a.a. *
73 a.a. *
Ligands
FAD ×2
HEC ×2
Metals
_CL ×2
Waters ×385
* Residue conservation analysis
PDB id:
1dii
Name: Oxidoreductase
Title: Crystal structure of p-cresol methylhydroxylase at 2.5 a resolution
Structure: P-cresol methylhydroxylase. Chain: a, b. Fragment: flavoprotein subunit. Synonym: pcmh. P-cresol methylhydroxylase. Chain: c, d. Fragment: cytochrome subunit. Synonym: pcmh. Ec: 1.17.99.1
Source: Pseudomonas putida. Organism_taxid: 303. Strain: ncimb 9869. Cellular_location: periplasm. Cellular_location: periplasm
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.172     R-free:   0.230
Authors: L.M.Cunane,Z.W.Chen,N.Shamala,F.S.Mathews,C.N.Cronin,W.S.Mcintire
Key ref:
L.M.Cunane et al. (2000). Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism. J Mol Biol, 295, 357-374. PubMed id: 10623531 DOI: 10.1006/jmbi.1999.3290
Date:
29-Nov-99     Release date:   08-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09788  (DH4C_PSEPU) -  4-cresol dehydrogenase [hydroxylating] flavoprotein subunit from Pseudomonas putida
Seq:
Struc: 		 
Seq:
Struc: 		521 a.a.
515 a.a.
Protein chains
Pfam   ArchSchema ?
P09787  (CY4C_PSEPU) -  4-cresol dehydrogenase [hydroxylating] cytochrome c subunit from Pseudomonas putida
Seq:
Struc: 		113 a.a.
73 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: Chains A, B: E.C.1.17.9.1  - 4-methylphenol dehydrogenase (hydroxylating).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-methylphenol + 4 oxidized [azurin] + H2O = 4 reduced [azurin] + 4-hydroxybenzaldehyde + 4 H+
4-methylphenol
 + 4 × oxidized [azurin]
 + H2O
 = 4 × reduced [azurin]
 + 4-hydroxybenzaldehyde
 + 4 × H(+)
   Enzyme class 3: Chains C, D: E.C.1.17.99.1  - Transferred entry: 1.17.9.1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-methylphenol + 2 acceptor + H2O = 4-hydroxybenzaldehyde + 2 reduced acceptor
4-methylphenol
 + 2 × acceptor
 + H(2)O
 = 4 × 4-hydroxybenzaldehyde
 + 2 × reduced acceptor
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1999.3290 J Mol Biol 295:357-374 (2000)
PubMed id: 10623531  
 
 
Structures of the flavocytochrome p-cresol methylhydroxylase and its enzyme-substrate complex: gated substrate entry and proton relays support the proposed catalytic mechanism.
L.M.Cunane, Z.W.Chen, N.Shamala, F.S.Mathews, C.N.Cronin, W.S.McIntire.
 
  ABSTRACT  
 
The degradation of the toxic phenol p-cresol by Pseudomonas bacteria occurs by way of the protocatechuate metabolic pathway. The first enzyme in this pathway, p-cresol methylhydroxylase (PCMH), is a flavocytochrome c. The enzyme first catalyzes the oxidation of p-cresol to p-hydroxybenzyl alcohol, utilizing one atom of oxygen derived from water, and yielding one molecule of reduced FAD. The reducing electron equivalents are then passed one at a time from the flavin cofactor to the heme cofactor by intramolecular electron transfer, and subsequently to cytochrome oxidase within the periplasmic membrane via one or more soluble electron carrier proteins. The product, p-hydroxybenzyl alcohol, can also be oxidized by PCMH to yield p-hydroxybenzaldehyde. The fully refined X-ray crystal structure of PCMH in the native state has been obtained at 2. 5 A resolution on the basis of the gene sequence. The structure of the enzyme-substrate complex has also been refined, at 2.75 A resolution, and reveals significant conformational changes in the active site upon substrate binding. The active site for substrate oxidation is deeply buried in the interior of the PCMH molecule. A route for substrate access to the site has been identified and is shown to be governed by a swinging-gate mechanism. Two possible proton transfer pathways, that may assist in activating the substrate for nucleophilic attack and in removal of protons generated during the reaction, have been revealed. Hydrogen bonding interactions between the flavoprotein and cytochrome subunits that stabilize the intramolecular complex and may contribute to the electron transfer process have been identified.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereo view of the PCMH heterotetramer as a ribbon drawing. The two flavoprotein subunits are in light and dark green, and the two cytochrome subunits are in red and yellow. The heme prosthetic groups are in red and the FAD groups are in gold. The molecular 2-fold axis is horizontal. Figure prepared using Ribbons [Carson 1997]. 		Figure 11.
Figure 11. Flavin and heme arrangement in PCMH. The light blue broken line indicates the most efficient electron transfer pathway according to the computer program GREENPATH (see the text). The green broken line represents the next most efficient pathway, and the pink and dark blue lines show the third most efficient pathways for the p-cresol bound and native enzymes, respectively. See Table 3.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 295, 357-374) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
19258534 M.Carmona, M.T.Zamarro, B.Blázquez, G.Durante-Rodríguez, J.F.Juárez, J.A.Valderrama, M.J.Barragán, J.L.García, and E.Díaz (2009).
Anaerobic catabolism of aromatic compounds: a genetic and genomic view.
  Microbiol Mol Biol Rev, 73, 71.  
19727923 M.E.Cristescu, and E.E.Egbosimba (2009).
Evolutionary history of D-lactate dehydrogenases: a phylogenomic perspective on functional diversity in the FAD binding oxidoreductase/transferase type 4 family.
  J Mol Evol, 69, 276-287.  
19333395 S.Sandhya, S.S.Rani, B.Pankaj, M.K.Govind, B.Offmann, N.Srinivasan, and R.Sowdhamini (2009).
Length variations amongst protein domain superfamilies and consequences on structure and function.
  PLoS ONE, 4, e4981.  
18658262 J.Johannes, A.Bluschke, N.Jehmlich, M.von Bergen, and M.Boll (2008).
Purification and characterization of active-site components of the putative p-cresol methylhydroxylase membrane complex from Geobacter metallireducens.
  J Bacteriol, 190, 6493-6500.  
18291320 P.Kallio, Z.Liu, P.Mäntsälä, J.Niemi, and M.Metsä-Ketelä (2008).
Sequential action of two flavoenzymes, PgaE and PgaM, in angucycline biosynthesis: chemoenzymatic synthesis of gaudimycin C.
  Chem Biol, 15, 157-166.  
18513323 T.Nishino, K.Okamoto, B.T.Eger, E.F.Pai, and T.Nishino (2008).
Mammalian xanthine oxidoreductase - mechanism of transition from xanthine dehydrogenase to xanthine oxidase.
  FEBS J, 275, 3278-3289.  
17449613 F.Peters, D.Heintz, J.Johannes, A.van Dorsselaer, and M.Boll (2007).
Genes, enzymes, and regulation of para-cresol metabolism in Geobacter metallireducens.
  J Bacteriol, 189, 4729-4738.  
17395717 I.Alexeev, A.Sultana, P.Mäntsälä, J.Niemi, and G.Schneider (2007).
Aclacinomycin oxidoreductase (AknOx) from the biosynthetic pathway of the antibiotic aclacinomycin is an unusual flavoenzyme with a dual active site.
  Proc Natl Acad Sci U S A, 104, 6170-6175.  
17419730 J.Jin, H.Mazon, R.H.van den Heuvel, D.B.Janssen, and M.W.Fraaije (2007).
Discovery of a eugenol oxidase from Rhodococcus sp. strain RHA1.
  FEBS J, 274, 2311-2321.  
16600599 A.Mattevi (2006).
To be or not to be an oxidase: challenging the oxygen reactivity of flavoenzymes.
  Trends Biochem Sci, 31, 276-283.  
16698554 J.H.Han, N.Kerrison, C.Chothia, and S.A.Teichmann (2006).
Divergence of interdomain geometry in two-domain proteins.
  Structure, 14, 935-945.  
15169773 R.H.van den Heuvel, W.A.van den Berg, S.Rovida, and W.J.van Berkel (2004).
Laboratory-evolved vanillyl-alcohol oxidase produces natural vanillin.
  J Biol Chem, 279, 33492-33500.
PDB codes: 1w1j 1w1k 1w1l 1w1m
12788775 D.J.Hopper, and L.Cottrell (2003).
Alkylphenol biotransformations catalyzed by 4-ethylphenol methylenehydroxylase.
  Appl Environ Microbiol, 69, 3650-3652.  
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
11761328 D.E.Edmondson, and P.Newton-Vinson (2001).
The covalent FAD of monoamine oxidase: structural and functional role and mechanism of the flavinylation reaction.
  Antioxid Redox Signal, 3, 789-806.  
11329284 I.Efimov, C.N.Cronin, and W.S.McIntire (2001).
Effects of noncovalent and covalent FAD binding on the redox and catalytic properties of p-cresol methylhydroxylase.
  Biochemistry, 40, 2155-2166.  
11133971 J.A.Müller, A.S.Galushko, A.Kappler, and B.Schink (2001).
Initiation of anaerobic degradation of p-cresol by formation of 4-hydroxybenzylsuccinate in desulfobacterium cetonicum.
  J Bacteriol, 183, 752-757.  
11747900 M.D.Krasowski, K.Nishikawa, N.Nikolaeva, A.Lin, and N.L.Harrison (2001).
Methionine 286 in transmembrane domain 3 of the GABAA receptor beta subunit controls a binding cavity for propofol and other alkylphenol general anesthetics.
  Neuropharmacology, 41, 952-964.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
10920192 R.H.van Den Heuvel, M.W.Fraaije, M.Ferrer, A.Mattevi, and W.J.van Berkel (2000).
Inversion of stereospecificity of vanillyl-alcohol oxidase.
  Proc Natl Acad Sci U S A, 97, 9455-9460.
PDB code: 1e0y
10809721 R.H.van den Heuvel, M.W.Fraaije, A.Mattevi, and W.J.van Berkel (2000).
Asp-170 is crucial for the redox properties of vanillyl-alcohol oxidase.
  J Biol Chem, 275, 14799-14808.
PDB code: 1dzn
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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