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(-) Description

Title :  CRYSTAL STRUCTURE OF SCYTALONE DEHYDRATASE F162A MUTANT IN THE UNLIGATED STATE
 
Authors :  M. Nakasako, T. Motoyama, I. Yamaguchi
Date :  04 Apr 01  (Deposition) - 08 Apr 03  (Release) - 11 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Lyase, Melanine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Motoyama, M. Nakasako, I. Yamaguchi
Crystallization Of Scytalone Dehydratase F162A Mutant In The Unligated State And A Preliminary X-Ray Diffraction Study At 37 K
Acta Crystallogr. , Sect. D V. 58 148 2002
PubMed-ID: 11752795  |  Reference-DOI: 10.1107/S0907444901017371
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SCYTALONE DEHYDRATASE
    Chains: A, B, C
    EC Number: 4.2.1.94
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: MAGNAPORTHE GRISEA
    Organism Taxid: 148305

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1IDP)

(-) Sites  (0, 0)

(no "Site" information available for 1IDP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IDP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IDP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IDP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IDP)

(-) Exons   (0, 0)

(no "Exon" information available for 1IDP)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:147
 aligned with SCYD_MAGO7 | P56221 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:147
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       
           SCYD_MAGO7     9 DEITFSDYLGLMTCVYEWADSYDSKDWDRLRKVIAPTLRIDYRSFLDKLWEAMPAEEFVGMVSSKQVLGDPTLRTQHFIGGTRWEKVSEDEVIGYHQLRVPHQRYKDTTMKEVTMKGHAHSANLHWYKKIDGVWKFAGLKPDIRWGE 155
               SCOP domains d1idpa_ A: Scytalone dehydratase                                                                                                                    SCOP domains
               CATH domains 1idpA00 A:9-155  [code=3.10.450.50, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhh.eeeeeehhhhhhhhhh........eee..eeeeeeeeeee..eeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1idp A   9 DEITFSDYLGLMTCVYEWADSYDSKDWDRLRKVIAPTLRIDYRSFLDKLWEAMPAEEFVGMVSSKQVLGDPTLRTQHFIGGTRWEKVSEDEVIGYHQLRVPHQRYKDTTMKEVTMKGHAHSANLHWYKKIDGVWKFAGLKPDIRWGE 155
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with SCYD_MAGO7 | P56221 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:147
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       
           SCYD_MAGO7     9 DEITFSDYLGLMTCVYEWADSYDSKDWDRLRKVIAPTLRIDYRSFLDKLWEAMPAEEFVGMVSSKQVLGDPTLRTQHFIGGTRWEKVSEDEVIGYHQLRVPHQRYKDTTMKEVTMKGHAHSANLHWYKKIDGVWKFAGLKPDIRWGE 155
               SCOP domains d1idpb_ B: Scytalone dehydratase                                                                                                                    SCOP domains
               CATH domains 1idpB00 B:9-155  [code=3.10.450.50, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhh.eeeeeehhhhhhhhhh........eee..eeeeeeeeeee..eeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1idp B   9 DEITFSDYLGLMTCVYEWADSYDSKDWDRLRKVIAPTLRIDYRSFLDKLWEAMPAEEFVGMVSSKQVLGDPTLRTQHFIGGTRWEKVSEDEVIGYHQLRVPHQRYKDTTMKEVTMKGHAHSANLHWYKKIDGVWKFAGLKPDIRWGE 155
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       


Chain C from PDB  Type:PROTEIN  Length:147
 aligned with SCYD_MAGO7 | P56221 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:147
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       
           SCYD_MAGO7     9 DEITFSDYLGLMTCVYEWADSYDSKDWDRLRKVIAPTLRIDYRSFLDKLWEAMPAEEFVGMVSSKQVLGDPTLRTQHFIGGTRWEKVSEDEVIGYHQLRVPHQRYKDTTMKEVTMKGHAHSANLHWYKKIDGVWKFAGLKPDIRWGE 155
               SCOP domains d1idpc_ C: Scytalone dehydratase                                                                                                                    SCOP domains
               CATH domains 1idpC00 C:9-155  [code=3.10.450.50, no name defined]                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhh.eeeeeehhhhhhhhhh........eee..eeeeeeeeeee..eeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1idp C   9 DEITFSDYLGLMTCVYEWADSYDSKDWDRLRKVIAPTLRIDYRSFLDKLWEAMPAEEFVGMVSSKQVLGDPTLRTQHFIGGTRWEKVSEDEVIGYHQLRVPHQRYKDTTMKEVTMKGHAHSANLHWYKKIDGVWKFAGLKPDIRWGE 155
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IDP)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (SCYD_MAGO7 | P56221)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0030411    scytalone dehydratase activity    Catalysis of the reaction: scytalone = 1,3,8-trihydroxynaphthalene + H(2)O.
biological process
    GO:0042438    melanin biosynthetic process    The chemical reactions and pathways resulting in the formation of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.
    GO:0006582    melanin metabolic process    The chemical reactions and pathways involving melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.
    GO:0043581    obsolete mycelium development    OBSOLETE. The process whose specific outcome is the progression of the mycelium over time, from its formation to the mature structure. A mycelium consists of a mass of branching, thread-like hyphae.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        SCYD_MAGO7 | P56221: 1std 2std 3std 4std 5std 6std 7std

(-) Related Entries Specified in the PDB File

3std 3STD CONTAINS THE SAME PROTEIN(WILD TYPE) COMPLEXES WITH CYANOCINNOLINE INHIBITOR
4std 4STD CONTAINS THE SAME PROTEIN(WILD TYPE)- INHIBITOR COMPLEXES CRYSTALLIZED AT PHYSIOLOGICAL PH
5std 5STD CONTAINS THE SAME PROTEIN(WILD TYPE) COMPLEXES WITH INHIBITOR 2
6std 6STD CONTAINS THE SAME PROTEIN(WILD TYPE) COMPLEXES WITH INHIBITOR 3
7std 7STD CONTAINS THE SAME PROTEIN(WILD TYPE) COMPLEXES WITH INHIBITOR 4