PDBsum entry 1std

Go to PDB code: 
protein ligands links
Lyase (carbon-oxygen) PDB id
Protein chain
162 a.a. *
Waters ×4
* Residue conservation analysis
PDB id:
Name: Lyase (carbon-oxygen)
Title: Crystal structure of scytalone dehydratase: a disease determ the rice pathogen, magnaporthe grisea
Structure: Scytalone dehydratase. Chain: a. Engineered: yes
Source: Magnaporthe grisea. Organism_taxid: 148305
Biol. unit: Trimer (from PQS)
2.90Å     R-factor:   0.179    
Authors: T.Lundqvist,Y.Lindqvist
Key ref:
T.Lundqvist et al. (1994). Crystal structure of scytalone dehydratase--a disease determinant of the rice pathogen, Magnaporthe grisea. Structure, 2, 937-944. PubMed id: 7866745 DOI: 10.1016/S0969-2126(94)00095-6
19-Aug-94     Release date:   19-Aug-95    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P56221  (SCYD_MAGO7) -  Scytalone dehydratase
172 a.a.
162 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Scytalone dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Scytalone = 1,3,8-trihydroxynaphthalene + H2O
= 1,3,8-trihydroxynaphthalene
+ H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     melanin metabolic process   3 terms 
  Biochemical function     lyase activity     2 terms  


    Added reference    
DOI no: 10.1016/S0969-2126(94)00095-6 Structure 2:937-944 (1994)
PubMed id: 7866745  
Crystal structure of scytalone dehydratase--a disease determinant of the rice pathogen, Magnaporthe grisea.
T.Lundqvist, J.Rice, C.N.Hodge, G.S.Basarab, J.Pierce, Y.Lindqvist.
BACKGROUND: Rice blast is caused by the pathogenic fungus,-Magnaporthe grisea. Non-pathogenic mutants have been identified that lack enzymes in the biosynthetic pathway of dihydroxynapthalene-derived melanin. These enzymes are therefore prime targets for fungicides designed to control rice blast disease. One of the enzymes identified by genetic analysis as a disease determinant is scytalone dehydratase. RESULTS: The three-dimensional structure of scytalone dehydratase in complex with a competitive inhibitor has been determined at 2.9 A resolution. A novel fold, a cone-shaped alpha + beta barrel, is adopted by the monomer in this trimeric protein, burying the hydrophobic active site in its interior. The interactions of the inhibitor with the protein side chains have been identified. The similarity of the inhibitor to the substrate and the side chains involved in binding afford some insights into possible catalytic mechanisms. CONCLUSIONS: These results provide a first look into the structure and catalytic residues of a non-metal dehydratase, a large class of hitherto structurally uncharacterized enzymes. It is envisaged that a detailed structural description of scytalone dehydratase will assist in the design of new inhibitors for controlling rice blast disease.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Reactions catalyzed by scytalone dehydratase. Conversion of scytalone (1) to 1,3,8-trihydroxynaphthalene (2); conversion of vermelone (3) to 1,8-dihydroxynapthalene (4); conversion of an artificial substrate (5) to an α ,β-unsaturated ketone (6). (b) Structure of salicylamide inhibitors; (R)-(+)-N-[1- (4-bromophenyl)ethyl]-5-fluorosalicylamide (7),N-(3,3-diphenylpropyl)-5-fluorosalicylamide (8) and (R)-(+)-N-[1-(4-iodophenyl)ethyl]-5-fluorosalicylamide (9). Figure 1. (a) Reactions catalyzed by scytalone dehydratase. Conversion of scytalone (1) to 1,3,8-trihydroxynaphthalene (2); conversion of vermelone (3) to 1,8-dihydroxynapthalene (4); conversion of an artificial substrate (5) to an α ,β-unsaturated ketone (6). (b) Structure of salicylamide inhibitors; (R)-(+)-N-[1- (4-bromophenyl)ethyl]-5-fluorosalicylamide (7),N-(3,3-diphenylpropyl)-5-fluorosalicylamide (8) and (R)-(+)-N-[1-(4-iodophenyl)ethyl]-5-fluorosalicylamide (9).
Figure 10.
Figure 10. Reaction mechanism based on a model where the substrate has been positioned in the active site so as to overlap with the analogous parts of the inhibitor. Figure 10. Reaction mechanism based on a model where the substrate has been positioned in the active site so as to overlap with the analogous parts of the inhibitor.
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 937-944) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19301315 C.Li, K.E.Roege, and W.L.Kelly (2009).
Analysis of the indanomycin biosynthetic gene cluster from Streptomyces antibioticus NRRL 8167.
  Chembiochem, 10, 1064-1072.  
19617363 Q.Zhang, F.Gao, H.Peng, H.Cheng, Y.Liu, J.Tang, J.Thompson, G.Wei, J.Zhang, Y.Du, J.Yan, and G.F.Gao (2009).
Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism.
  J Bacteriol, 191, 5832-5837.
PDB codes: 3dbn 3fvm
17681008 I.Engh, M.Nowrousian, and U.Kück (2007).
Regulation of melanin biosynthesis via the dihydroxynaphthalene pathway is dependent on sexual development in the ascomycete Sordaria macrospora.
  FEMS Microbiol Lett, 275, 62-70.  
18084070 N.Handa, S.Kishishita, S.Morita, R.Akasaka, Z.Jin, J.Chrzas, L.Chen, Z.J.Liu, B.C.Wang, S.Sugano, A.Tanaka, T.Terada, M.Shirouzu, and S.Yokoyama (2007).
Structure of the human Tim44 C-terminal domain in complex with pentaethylene glycol: ligand-bound form.
  Acta Crystallogr D Biol Crystallogr, 63, 1225-1234.
PDB code: 2cw9
16632258 A.R.Gallimore, C.B.Stark, A.Bhatt, B.M.Harvey, Y.Demydchuk, V.Bolanos-Garcia, D.J.Fowler, J.Staunton, P.F.Leadlay, and J.B.Spencer (2006).
Evidence for the role of the monB genes in polyether ring formation during monensin biosynthesis.
  Chem Biol, 13, 453-460.  
15071504 A.Sultana, P.Kallio, A.Jansson, J.S.Wang, J.Niemi, P.Mäntsälä, and G.Schneider (2004).
Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.
  EMBO J, 23, 1911-1921.
PDB code: 1sjw
15056895 N.Yamada, T.Motoyama, M.Nakasako, S.Kagabu, T.Kudo, and I.Yamaguchi (2004).
Enzymatic characterization of scytalone dehydratase Val75Met variant found in melanin biosynthesis dehydratase inhibitor (MBI-D) resistant strains of the rice blast fungus.
  Biosci Biotechnol Biochem, 68, 615-621.  
12773375 M.Arand, B.M.Hallberg, J.Zou, T.Bergfors, F.Oesch, M.J.van der Werf, Bont, T.A.Jones, and S.L.Mowbray (2003).
Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site.
  EMBO J, 22, 2583-2592.
PDB codes: 1nu3 1nww
12835756 S.Fribourg, and E.Conti (2003).
Structural similarity in the absence of sequence homology of the messenger RNA export factors Mtr2 and p15.
  EMBO Rep, 4, 699-703.
PDB code: 1of5
12389036 D.Lim, and N.C.Strynadka (2002).
Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus.
  Nat Struct Biol, 9, 870-876.
PDB codes: 1mwr 1mws 1mwt 1mwu 1mwx 1vqq
11746694 Y.Nagata, K.Mori, M.Takagi, A.G.Murzin, and J.Damborský (2001).
Identification of protein fold and catalytic residues of gamma-hexachlorocyclohexane dehydrochlorinase LinA.
  Proteins, 45, 471-477.  
10694394 D.B.Jordan, Y.J.Zheng, B.A.Lockett, and G.S.Basarab (2000).
Stereochemistry of the enolization of scytalone by scytalone dehydratase.
  Biochemistry, 39, 2276-2282.  
10097077 A.E.Nixon, S.M.Firestine, F.G.Salinas, and S.J.Benkovic (1999).
Rational design of a scytalone dehydratase-like enzyme using a structurally homologous protein scaffold.
  Proc Natl Acad Sci U S A, 96, 3568-3571.  
10551849 H.S.Cho, N.C.Ha, G.Choi, H.J.Kim, D.Lee, K.S.Oh, K.S.Kim, W.Lee, K.Y.Choi, and B.H.Oh (1999).
Crystal structure of delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization.
  J Biol Chem, 274, 32863-32868.
PDB code: 1qjg
10382670 Z.Wawrzak, T.Sandalova, J.J.Steffens, G.S.Basarab, T.Lundqvist, Y.Lindqvist, and D.B.Jordan (1999).
High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH.
  Proteins, 35, 425-439.
PDB codes: 4std 5std 6std 7std
9666335 A.G.Murzin (1998).
How far divergent evolution goes in proteins.
  Curr Opin Struct Biol, 8, 380-387.  
9634695 B.Kauppi, K.Lee, E.Carredano, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (1998).
Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
  Structure, 6, 571-586.
PDB code: 1ndo
9665698 M.Nakasako, T.Motoyama, Y.Kurahashi, and I.Yamaguchi (1998).
Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition.
  Biochemistry, 37, 9931-9939.
PDB code: 2std
9571787 T.Motoyama, K.Imanishi, and I.Yamaguchi (1998).
cDNA cloning, expression, and mutagenesis of scytalone dehydratase needed for pathogenicity of the rice blast fungus, Pyricularia oryzae.
  Biosci Biotechnol Biochem, 62, 564-566.  
9539706 Y.J.Zheng, and T.C.Bruice (1998).
Role of a critical water in scytalone dehydratase-catalyzed reaction.
  Proc Natl Acad Sci U S A, 95, 4158-4163.  
9369474 S.W.Kim, S.S.Cha, H.S.Cho, J.S.Kim, N.C.Ha, M.J.Cho, S.Joo, K.K.Kim, K.Y.Choi, and B.H.Oh (1997).
High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.
  Biochemistry, 36, 14030-14036.
PDB codes: 1oh0 1opy 4tsu
8860003 A.Andersson, D.Jordan, G.Schneider, B.Valent, and Y.Lindqvist (1996).
Crystallization and preliminary x-ray diffraction study of 1 ,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea.
  Proteins, 24, 525-527.  
8939741 A.Andersson, D.Jordan, G.Schneider, and Y.Lindqvist (1996).
Crystal structure of the ternary complex of 1,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea with NADPH and an active-site inhibitor.
  Structure, 4, 1161-1170.
PDB code: 1ybv
8804825 A.G.Murzin (1996).
Structural classification of proteins: new superfamilies.
  Curr Opin Struct Biol, 6, 386-394.  
8805534 M.Leesong, B.S.Henderson, J.R.Gillig, J.M.Schwab, and J.L.Smith (1996).
Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site.
  Structure, 4, 253-264.
PDB codes: 1mka 1mkb
8905089 R.J.Howard, and B.Valent (1996).
Breaking and entering: host penetration by the fungal rice blast pathogen Magnaporthe grisea.
  Annu Rev Microbiol, 50, 491-512.  
8944775 S.Köster, G.Stier, R.Ficner, M.Hölzer, H.C.Curtius, D.Suck, and S.Ghisla (1996).
Location of the active site and proposed catalytic mechanism of pterin-4a-carbinolamine dehydratase.
  Eur J Biochem, 241, 858-864.  
  8953707 Y.Kubo, Y.Takano, N.Endo, N.Yasuda, S.Tajima, and I.Furusawa (1996).
Cloning and structural analysis of the melanin biosynthesis gene SCD1 encoding scytalone dehydratase in Colletotrichum lagenarium.
  Appl Environ Microbiol, 62, 4340-4344.  
8618906 G.Johnen, D.Kowlessur, B.A.Citron, and S.Kaufman (1995).
Characterization of the wild-type form of 4a-carbinolamine dehydratase and two naturally occurring mutants associated with hyperphenylalaninemia.
  Proc Natl Acad Sci U S A, 92, 12384-12388.  
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.