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PDBsum entry 1io8
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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1io8

 

 

 

 

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Contents
Protein chains
366 a.a. *
Ligands
HEM ×2
Waters ×283
* Residue conservation analysis
PDB id:
1io8
Name: Oxidoreductase
Title: Thermophilic cytochrome p450 (cyp119) from sulfolobus solfataricus: high resolution structural origin of its thermostability and functional properties
Structure: Cytochrome p450 cyp119. Chain: a, b. Engineered: yes. Mutation: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.230     R-free:   0.307
Authors: S.-Y.Park,K.Yamane,S.Adachi,Y.Shiro,S.G.Sligar,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref: S.Y.Park et al. (2002). Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties. J Inorg Biochem, 91, 491-501. PubMed id: 12237217
Date:
08-Feb-01     Release date:   07-Mar-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q55080  (CP119_SULAC) -  Cytochrome P450 119 from Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
Seq:
Struc: 		368 a.a.
366 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 1: E.C.1.11.1.7  - peroxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2 a phenolic donor + H2O2 = 2 a phenolic radical donor + 2 H2O
2 × a phenolic donor
 + H2O2
 = 2 × a phenolic radical donor
 + 2 × H2O
      Cofactor: Heme
Heme
Bound ligand (Het Group name = HEM) matches with 95.45% similarity
   Enzyme class 2: E.C.1.14.-.-
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
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

 

 
    Added reference    
 
 
J Inorg Biochem 91:491-501 (2002)
PubMed id: 12237217  
 
 
Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties.
S.Y.Park, K.Yamane, S.Adachi, Y.Shiro, K.E.Weiss, S.A.Maves, S.G.Sligar.
 
  ABSTRACT  
 
Crystal structures of a thermostable cytochrome P450 (CYP119) and a site-directed mutant, (Phe24Leu), from the acidothermophilic archaea Sulfolobus solfataricus were determined at 1.5-2.0 A resolution. We identify important crystallographic waters in the ferric heme pocket, observe protein conformational changes upon inhibitor binding, and detect a unique distribution of surface charge not found in other P450s. An analysis of factors contributing to thermostability of CYP119 of these high resolution structures shows an apparent increase in clustering of aromatic residues and optimum stacking. The contribution of aromatic stacking was investigated further with the mutant crystal structure and differential scanning calorimetry.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21264369 E.O'Reilly, V.Köhler, S.L.Flitsch, and N.J.Turner (2011).
Cytochromes P450 as useful biocatalysts: addressing the limitations.
  Chem Commun (Camb), 47, 2490-2501.  
21359359 H.Matsumura, K.Matsuda, N.Nakamura, A.Ohtaki, H.Yoshida, S.Kamitori, M.Yohda, and H.Ohno (2011).
Monooxygenation by a thermophilic cytochrome P450 via direct electron donation from NADH.
  Metallomics, 3, 389-395.  
21356195 R.Brandman, J.N.Lampe, Y.Brandman, and P.R.de Montellano (2011).
Active-site residues move independently from the rest of the protein in a 200 ns molecular dynamics simulation of cytochrome P450 CYP119.
  Arch Biochem Biophys, 509, 127-132.  
21171581 Y.T.Lee, E.C.Glazer, R.F.Wilson, C.D.Stout, and D.B.Goodin (2011).
Three clusters of conformational States in p450cam reveal a multistep pathway for closing of the substrate access channel .
  Biochemistry, 50, 693-703.  
19635450 H.Ouellet, J.B.Johnston, and P.R.Ortiz de Montellano (2010).
The Mycobacterium tuberculosis cytochrome P450 system.
  Arch Biochem Biophys, 493, 82-95.  
20632328 K.S.Rabe, M.Erkelenz, K.Kiko, and C.M.Niemeyer (2010).
Peroxidase activity of bacterial cytochrome P450 enzymes: modulation by fatty acids and organic solvents.
  Biotechnol J, 5, 891-899.  
19947890 N.Shakunthala (2010).
New cytochrome P450 mechanisms: implications for understanding molecular basis for drug toxicity at the level of the cytochrome.
  Expert Opin Drug Metab Toxicol, 6, 1.  
19769330 P.R.Ortiz de Montellano (2010).
Hydrocarbon hydroxylation by cytochrome P450 enzymes.
  Chem Rev, 110, 932-948.  
20446763 T.C.Pochapsky, S.Kazanis, and M.Dang (2010).
Conformational plasticity and structure/function relationships in cytochromes P450.
  Antioxid Redox Signal, 13, 1273-1296.  
20950270 W.Yang, S.G.Bell, H.Wang, W.Zhou, M.Bartlam, L.L.Wong, and Z.Rao (2010).
The structure of CYP101D2 unveils a potential path for substrate entry into the active site.
  Biochem J, 433, 85-93.
PDB codes: 3nv5 3nv6
20297780 Y.T.Lee, R.F.Wilson, I.Rupniewski, and D.B.Goodin (2010).
P450cam visits an open conformation in the absence of substrate.
  Biochemistry, 49, 3412-3419.
PDB codes: 3l61 3l62 3l63
19555717 I.G.Denisov, D.J.Frank, and S.G.Sligar (2009).
Cooperative properties of cytochromes P450.
  Pharmacol Ther, 124, 151-167.  
19074393 L.H.Xu, S.Fushinobu, H.Ikeda, T.Wakagi, and H.Shoun (2009).
Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state.
  J Bacteriol, 191, 1211-1219.
PDB codes: 3e5j 3e5k 3e5l
19397311 S.C.Gay, L.Sun, K.Maekawa, J.R.Halpert, and C.D.Stout (2009).
Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through alpha-helical repositioning.
  Biochemistry, 48, 4762-4771.
PDB codes: 3g5n 3g93
19348026 T.Mandai, S.Fujiwara, and S.Imaoka (2009).
A novel electron transport system for thermostable CYP175A1 from Thermus thermophilus HB27.
  FEBS J, 276, 2416-2429.  
18830657 C.Virus, and R.Bernhardt (2008).
Molecular evolution of a steroid hydroxylating cytochrome p450 using a versatile steroid detection system for screening.
  Lipids, 43, 1133-1141.  
18157853 K.S.Rabe, K.Kiko, and C.M.Niemeyer (2008).
Characterization of the peroxidase activity of CYP119, a thermostable P450 from Sulfolobus acidocaldarius.
  Chembiochem, 9, 420-425.  
18174331 M.Newcomb, J.A.Halgrimson, J.H.Horner, E.C.Wasinger, L.X.Chen, and S.G.Sligar (2008).
X-ray absorption spectroscopic characterization of a cytochrome P450 compound II derivative.
  Proc Natl Acad Sci U S A, 105, 8179-8184.  
17534532 A.W.Munro, H.M.Girvan, and K.J.McLean (2007).
Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily.
  Nat Prod Rep, 24, 585-609.  
17585868 G.I.Lepesheva, M.Seliskar, C.G.Knutson, N.V.Stourman, D.Rozman, and M.R.Waterman (2007).
Conformational dynamics in the F/G segment of CYP51 from Mycobacterium tuberculosis monitored by FRET.
  Arch Biochem Biophys, 464, 221-227.  
16439365 B.K.Muralidhara, S.Negi, C.C.Chin, W.Braun, and J.R.Halpert (2006).
Conformational flexibility of mammalian cytochrome P450 2B4 in binding imidazole inhibitors with different ring chemistry and side chains. Solution thermodynamics and molecular modeling.
  J Biol Chem, 281, 8051-8061.  
16825192 D.H.Sherman, S.Li, L.V.Yermalitskaya, Y.Kim, J.A.Smith, M.R.Waterman, and L.M.Podust (2006).
The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae.
  J Biol Chem, 281, 26289-26297.
PDB codes: 2bvj 2c6h 2c7x 2cd8
15858262 Y.Eisenberg-Domovich, V.P.Hytönen, M.Wilchek, E.A.Bayer, M.S.Kulomaa, and O.Livnah (2005).
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
  Acta Crystallogr D Biol Crystallogr, 61, 528-538.
PDB codes: 1y52 1y53 1y55
15100217 E.E.Scott, M.A.White, Y.A.He, E.F.Johnson, C.D.Stout, and J.R.Halpert (2004).
Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding.
  J Biol Chem, 279, 27294-27301.
PDB code: 1suo
14691240 L.M.Podust, H.Bach, Y.Kim, D.C.Lamb, M.Arase, D.H.Sherman, S.L.Kelly, and M.R.Waterman (2004).
Comparison of the 1.85 A structure of CYP154A1 from Streptomyces coelicolor A3(2) with the closely related CYP154C1 and CYPs from antibiotic biosynthetic pathways.
  Protein Sci, 13, 255-268.
PDB code: 1odo
15189165 O.Pylypenko, and I.Schlichting (2004).
Structural aspects of ligand binding to and electron transfer in bacterial and fungal P450s.
  Annu Rev Biochem, 73, 991.  
15256616 P.A.Williams, J.Cosme, D.M.Vinkovic, A.Ward, H.C.Angove, P.J.Day, C.Vonrhein, I.J.Tickle, and H.Jhoti (2004).
Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone.
  Science, 305, 683-686.
PDB codes: 1w0e 1w0f 1w0g
12519760 D.S.Lee, A.Yamada, H.Sugimoto, I.Matsunaga, H.Ogura, K.Ichihara, S.Adachi, S.Y.Park, and Y.Shiro (2003).
Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis. Crystallographic, spectroscopic, and mutational studies.
  J Biol Chem, 278, 9761-9767.
PDB code: 1izo
12401810 J.K.Yano, F.Blasco, H.Li, R.D.Schmid, A.Henne, and T.L.Poulos (2003).
Preliminary characterization and crystal structure of a thermostable cytochrome P450 from Thermus thermophilus.
  J Biol Chem, 278, 608-616.
PDB code: 1n97
12943843 J.K.Yano, and T.L.Poulos (2003).
New understandings of thermostable and peizostable enzymes.
  Curr Opin Biotechnol, 14, 360-365.  
12964165 O.Salazar, P.C.Cirino, and F.H.Arnold (2003).
Thermostabilization of a cytochrome p450 peroxygenase.
  Chembiochem, 4, 891-893.  
14597705 T.L.Poulos (2003).
Cytochrome P450 flexibility.
  Proc Natl Acad Sci U S A, 100, 13121-13122.  
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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