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(-) Description

Title :  STRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADPH AND AN ACTIVE SITE INHIBITOR
 
Authors :  A. Andersson, G. Schneider, Y. Lindqvist
Date :  23 Sep 96  (Deposition) - 15 Oct 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Andersson, D. Jordan, G. Schneider, Y. Lindqvist
Crystal Structure Of The Ternary Complex Of 1, 3, 8-Trihydroxynaphthalene Reductase From Magnaporthe Grisea With Nadph And An Active-Site Inhibitor.
Structure V. 4 1161 1996
PubMed-ID: 8939741  |  Reference-DOI: 10.1016/S0969-2126(96)00124-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRIHYDROXYNAPHTHALENE REDUCTASE
    Cell Line: BL21
    Chains: A, B
    EC Number: 1.3.1.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: BUF+
    Expression System Plasmid: PTHNR2
    Expression System Strain: BL21 (DE3) PET11 (NOVAGEN)
    Expression System Taxid: 562
    Gene: BUF+
    Mutation: YES
    Organism Scientific: MAGNAPORTHE GRISEA
    Organism Taxid: 148305
    Strain: 409158
    Synonym: NAPHTHOL REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1BEA2Ligand/Ion5-METHYL-1,2,4-TRIAZOLO[3,4-B]BENZOTHIAZOLE
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1BEA4Ligand/Ion5-METHYL-1,2,4-TRIAZOLO[3,4-B]BENZOTHIAZOLE
2NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1A1UNKNOWNVAL A:118 , SER A:164 , ILE A:165 , TYR A:178 , GLY A:210 , MET A:215 , VAL A:219 , CYS A:220 , TYR A:223 , TRP A:243 , MET A:283CATALYTIC SITE.
2A2UNKNOWNARG A:39 , ILE A:41 , ALA A:61 , ASN A:62 , SER A:63 , VAL A:88 , ASN A:114 , SER A:115 , TYR A:178 , LYS A:182 , ILE A:211 , THR A:213COFACTOR BINDING SITE.
3AC1SOFTWAREGLY A:36 , ARG A:39 , GLY A:40 , ILE A:41 , ALA A:61 , ASN A:62 , SER A:63 , ALA A:86 , ASN A:87 , VAL A:88 , ASN A:114 , SER A:115 , GLY A:116 , MET A:162 , GLY A:163 , SER A:164 , TYR A:178 , LYS A:182 , PRO A:208 , GLY A:210 , ILE A:211 , THR A:213 , MET A:215 , BEA A:285BINDING SITE FOR RESIDUE NDP A 284
4AC2SOFTWARESER A:164 , ILE A:165 , TYR A:178 , GLY A:210 , MET A:215 , TYR A:223 , NDP A:284BINDING SITE FOR RESIDUE BEA A 285
5AC3SOFTWAREGLY B:36 , ARG B:39 , GLY B:40 , ILE B:41 , ALA B:61 , ASN B:62 , SER B:63 , ALA B:86 , ASN B:87 , VAL B:88 , ASN B:114 , SER B:115 , GLY B:116 , MET B:162 , GLY B:163 , SER B:164 , TYR B:178 , LYS B:182 , PRO B:208 , GLY B:210 , ILE B:211 , THR B:213 , MET B:215 , BEA B:285BINDING SITE FOR RESIDUE NDP B 284
6AC4SOFTWARESER B:164 , ILE B:165 , TYR B:178 , GLY B:210 , MET B:215 , TYR B:223 , NDP B:284BINDING SITE FOR RESIDUE BEA B 285
7B1UNKNOWNVAL B:118 , SER B:164 , ILE B:165 , TYR B:178 , GLY B:210 , MET B:215 , VAL B:219 , CYS B:220 , TYR B:223 , TRP B:243 , MET B:283CATALYTIC SITE.
8B2UNKNOWNARG B:39 , ILE B:41 , ALA B:61 , ASN B:62 , SER B:63 , VAL B:88 , ASN B:114 , SER B:115 , TYR B:178 , LYS B:182 , ILE B:211 , THR B:213COFACTOR BINDING SITE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.T4HR_MAGO7165-193
 		  2A:165-193
B:165-193
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.T4HR_MAGO7165-193
 		  4A:165-193
B:165-193

(-) Exons   (0, 0)

(no "Exon" information available for 1YBV)

(-) Sequences/Alignments

Asymmetric 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:270
 aligned with T4HR_MAGO7 | Q12634 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:270
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
           T4HR_MAGO7    14 DAIPGPLGPQSASLEGKVALVTGAGRGIGREMAMELGRRGCKVIVNYANSTESAEEVVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFTINTRGQFFVAREAYKHLEIGGRLILMGSITGQAKAVPKHAVYSGSKGAIETFARCMAIDMADKKITVNVVAPGGIKTDMYHAVCREYIPNGENLSNEEVDEYAASAWSPLHRVGLPIDIARVVCFLASNDGGWVTGKVIGIDGGACM 283
               SCOP domains d1ybva_ A: 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase)                                                                                                                                                                                                      SCOP domains
               CATH domains 1ybvA00 A:14-283 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhh....eeeee.....hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh....eeee.........hhh..hhhhhhhhhhh.hhhhhhhhhhhhh.....eeeee..hhh........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhh.........hhhhhhhhhhh.........hhhhhhhhhhhh.hhhhh...eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:165-193    ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ybv A  14 DAIPGPLGPQSASLEGKVALVTGAGRGIGREMAMELGRRGCKVIVNYANSTESAEEVVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFTINTRGQFFVAREAYKHLEIGGRLILMGSITGQAKAVPKHAVYSGSKGAIETFARCMAIDMADKKITVNVVAPGGIKTDMYHAVCREYIPNGENLSNEEVDEYAAVQWSPLRRVGLPIDIARVVCFLASNDGGWVTGKVIGIDGGACM 283
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283


Chain B from PDB  Type:PROTEIN  Length:270
 aligned with T4HR_MAGO7 | Q12634 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:270
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
           T4HR_MAGO7    14 DAIPGPLGPQSASLEGKVALVTGAGRGIGREMAMELGRRGCKVIVNYANSTESAEEVVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFTINTRGQFFVAREAYKHLEIGGRLILMGSITGQAKAVPKHAVYSGSKGAIETFARCMAIDMADKKITVNVVAPGGIKTDMYHAVCREYIPNGENLSNEEVDEYAASAWSPLHRVGLPIDIARVVCFLASNDGGWVTGKVIGIDGGACM 283
               SCOP domains d1ybvb_ B: 1,3,8-trihydroxynaphtalene reductase (THNR, naphtol reductase)                                                                                                                                                                                                      SCOP domains
               CATH domains 1ybvB00 B:14-283 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----------------adh_short-1ybvB01 B:30-197                                                                                                                                              -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------adh_short-1ybvB02 B:30-197                                                                                                                                              -------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........hhhh....eeeee.....hhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh....eeee.........hhh..hhhhhhhhhhh.hhhhhhhhhhhhh.....eeeee..hhh........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhh.........hhhhhhhhhhh.........hhhhhhhhhhhh.hhhhh...eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:165-193    ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ybv B  14 DAIPGPLGPQSASLEGKVALVTGAGRGIGREMAMELGRRGCKVIVNYANSTESAEEVVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFTINTRGQFFVAREAYKHLEIGGRLILMGSITGQAKAVPKHAVYSGSKGAIETFARCMAIDMADKKITVNVVAPGGIKTDMYHAVCREYIPNGENLSNEEVDEYAAVQWSPLRRVGLPIDIARVVCFLASNDGGWVTGKVIGIDGGACM 283
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (T4HR_MAGO7 | Q12634)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0047039    tetrahydroxynaphthalene reductase activity    Catalysis of the reaction: NADP+ + scytalone = NADPH + H+ + 1,3,6,8-naphthalenetetrol.
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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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  1.3.1.50
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 Related Entries

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

UniProtKB/Swiss-Prot
        T4HR_MAGO7 | Q12634: 1doh 1g0n 1g0o

(-) Related Entries Specified in the PDB File

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