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(-) Description

Title :  CRYSTAL STRUCTURE OF 1,3,6,8-TETRAHYDROXYNAPHTHALENE SYNTHASE (THNS) FROM STREPTOMYCES COELICOLOR A3(2): A BACTERIAL TYPE III POLYKETIDE SYNTHASE (PKS) PROVIDES INSIGHTS INTO ENZYMATIC CONTROL OF REACTIVE POLYKETIDE INTERMEDIATES
 
Authors :  M. B. Austin, M. Izumikawa, M. E. Bowman, D. W. Udwary, J. L. Ferrer, B. S. J. P. Noel
Date :  13 Jul 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Type Iii Polyketide Synthase, Pks, Bacterial, Thiolase Fold, Alpha- Beta-Alpha-Beta-Alpha Fold, Catalytic Triad, Chs-Like, Thns, Tetrahydroxynaphthalene Synthase, Chalcone/Stilbene Synthase Superfamily, Malonyl-Coa, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. B. Austin, M. Izumikawa, M. E. Bowman, D. W. Udwary, J. L. Ferrer, B. S. Moore, J. P. Noel
Crystal Structure Of A Bacterial Type Iii Polyketide Synthase And Enzymatic Control Of Reactive Polyketide Intermediates
J. Biol. Chem. V. 279 45162 2004
PubMed-ID: 15265863  |  Reference-DOI: 10.1074/JBC.M406567200

(-) Compounds

Molecule 1 - PUTATIVE POLYKETIDE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PHIS8
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SCO1206
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 100226
    Strain: A3(2)

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
115P2Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:28 , HIS A:29 , CYS A:168 , SER A:169 , CYS A:171 , TYR A:172 , ASN A:185 , PHE A:188 , TYR A:224BINDING SITE FOR RESIDUE 15P A 1000
2AC2SOFTWAREARG B:28 , HIS B:29 , CYS B:168 , TYR B:172 , ASN B:185 , PHE B:188 , GOL B:4000 , HOH B:4004BINDING SITE FOR RESIDUE 15P B 3000
3AC3SOFTWARECYS A:171 , TYR A:172 , GLN A:173 , ASP A:176 , ASN A:185 , PHE A:231 , HIS A:232 , PHE A:233BINDING SITE FOR RESIDUE GOL A 2000
4AC4SOFTWARECYS B:171 , TYR B:172 , GLN B:173 , ASP B:176 , SER B:181 , ASN B:185 , PHE B:231 , HIS B:232 , PHE B:233 , 15P B:3000BINDING SITE FOR RESIDUE GOL B 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U0M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Met A:111 -Pro A:112
2Gly A:336 -Ile A:337
3Met B:111 -Pro B:112
4Gly B:336 -Ile B:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U0M)

(-) Exons   (0, 0)

(no "Exon" information available for 1U0M)

(-) 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:348
 aligned with RPPA_STRCO | Q9FCA7 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:348
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341        
           RPPA_STRCO     2 ATLCRPSVSVPEHVITMEETLELARRRHTDHPQLPLALRLIENTGVRTRHIVQPIEDTLEHPGFEDRNKVYEREAKSRVPAVIQRALDDAELLATDIDVIIYVSCTGFMMPSLTAWLINEMGFDSTTRQIPIAQLGCAAGGAAINRAHDFCTAYPEANALIVACEFCSLCYQPTDLGVGSLLCNGLFGDGIAAAVVRGRGGTGVRLERNGSYLIPKTEDWIMYDVKATGFHFLLDKRVPATMEPLAPALKELAGEHGWDASDLDFYIVHAGGPRILDDLSTFLEVDPHAFRFSRATLTEYGNIASAVVLDALRRLFDEGGVEEGARGLLAGFGPGITAEMSLGCWQTA 349
               SCOP domains d1u0ma1 A:2-201 Putative polyketide synthase SCO1206                                                                                                                                                    d1u0ma2 A:202-349 Putative polyketide synthase SCO1206                                                                                               SCOP domains
               CATH domains 1u0mA01 A:2-203  [code=3.40.47.10, no name defined]                                                                                                                                                       1u0mA02 A:204-349  [code=3.40.47.10, no name defined]                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee...eee...eeeehhhhhhhhhhhhh...hhhhhhhhhhhh...eeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeee........hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhh.....hhhhhhhhhhh.eeeeeeeee.....eeeeeeeeeee.......eeeeee..eeeeee...hhhhhhhhhhhhhhhhhh...........eee.hhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.........eeeeee...eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u0m A   2 ATLCRPSVSVPEHVITMEETLELARRRHTDHPQLPLALRLIENTGVRTRHIVQPIEDTLEHPGFEDRNKVYEREAKSRVPAVIQRALDDAELLATDIDVIIYVSCTGFMMPSLTAWLINEMGFDSTTRQIPIAQLGCAAGGAAINRAHDFCTAYPEANALIVACEFCSLCYQPTDLGVGSLLCNGLFGDGIAAAVVRGRGGTGVRLERNGSYLIPKTEDWIMYDVKATGFHFLLDKRVPATMEPLAPALKELAGEHGWDASDLDFYIVHAGGPRILDDLSTFLEVDPHAFRFSRATLTEYGNIASAVVLDALRRLFDEGGVEEGARGLLAGFGPGITAEMSLGCWQTA 349
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341        


Chain B from PDB  Type:PROTEIN  Length:348
 aligned with RPPA_STRCO | Q9FCA7 from UniProtKB/Swiss-Prot  Length:374

    Alignment length:348
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341        
           RPPA_STRCO     2 ATLCRPSVSVPEHVITMEETLELARRRHTDHPQLPLALRLIENTGVRTRHIVQPIEDTLEHPGFEDRNKVYEREAKSRVPAVIQRALDDAELLATDIDVIIYVSCTGFMMPSLTAWLINEMGFDSTTRQIPIAQLGCAAGGAAINRAHDFCTAYPEANALIVACEFCSLCYQPTDLGVGSLLCNGLFGDGIAAAVVRGRGGTGVRLERNGSYLIPKTEDWIMYDVKATGFHFLLDKRVPATMEPLAPALKELAGEHGWDASDLDFYIVHAGGPRILDDLSTFLEVDPHAFRFSRATLTEYGNIASAVVLDALRRLFDEGGVEEGARGLLAGFGPGITAEMSLGCWQTA 349
               SCOP domains d1u0mb1 B:2-201 Putative polyketide synthase SCO1206                                                                                                                                                    d1u0mb2 B:202-349 Putative polyketide synthase SCO1206                                                                                               SCOP domains
               CATH domains 1u0mB01 B:2-203  [code=3.40.47.10, no name defined]                                                                                                                                                       1u0mB02 B:204-349  [code=3.40.47.10, no name defined]                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..eee...eeeehhhhhhhhhhhh....hhhhhhhhhhhh...eeee..hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeee........hhhhhhhhhh......eeeee..hhhhhhhhhhhhhhhhhhhh...eeeeeeeee.hhhh.....hhhhhhhhhhh.eeeeeeeee.....eee...eeeee.......eeeeee..eeeeee...hhhhhhhhhhhhhhhhhh..........eeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........eeeeee...eeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u0m B   2 ATLCRPSVSVPEHVITMEETLELARRRHTDHPQLPLALRLIENTGVRTRHIVQPIEDTLEHPGFEDRNKVYEREAKSRVPAVIQRALDDAELLATDIDVIIYVSCTGFMMPSLTAWLINEMGFDSTTRQIPIAQLGCAAGGAAINRAHDFCTAYPEANALIVACEFCSLCYQPTDLGVGSLLCNGLFGDGIAAAVVRGRGGTGVRLERNGSYLIPKTEDWIMYDVKATGFHFLLDKRVPATMEPLAPALKELAGEHGWDASDLDFYIVHAGGPRILDDLSTFLEVDPHAFRFSRATLTEYGNIASAVVLDALRRLFDEGGVEEGARGLLAGFGPGITAEMSLGCWQTA 349
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1U0M)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RPPA_STRCO | Q9FCA7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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