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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL TYPE III POLYKETIDE SYNTHASE (PKS III) DOMAIN OF 'STEELY1' (A TYPE I/III PKS HYBRID FROM DICTYOSTELIUM)
 
Authors :  M. B. Austin, T. Saito, M. E. Bowman, S. Haydock, A. Kato, B. S. Moore, R. R J. P. Noel
Date :  06 Jun 06  (Deposition) - 22 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thiolase-Fold, Type Iii Polyketide Synthase, Pks, Chalcone-Stilbene Synthase Superfamily, Type I Pks, Type I Fatty Acid Synthase, Fas, Biosynthetic Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. B. Austin, T. Saito, M. E. Bowman, S. Haydock, A. Kato, B. S. Moore, R. R. Kay, J. P. Noel
Biosynthesis Of Dictyostelium Discoideum Differentiation-Inducing Factor By A Hybrid Type I Fatty Acid-Type Iii Polyketide Synthase.
Nat. Chem. Biol. V. 2 494 2006
PubMed-ID: 16906151  |  Reference-DOI: 10.1038/NCHEMBIO811

(-) Compounds

Molecule 1 - STEELY1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS-8, PET28 DERIVATIVE
    Expression System StrainBL21(DE3)/CODONPLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentENZYMATIC DOMAIN, RESIDUES 2776-3147
    Organism ScientificDICTYOSTELIUM DISCOIDEUM
    Organism Taxid352472
    StrainAX4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1P6G1Ligand/IonHEXAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:101 , CYS A:2930 , ASP A:2968 , GLY A:2969 , GLY A:2970 , ASP A:2971 , MET A:3017 , ALA A:3032 , ILE A:3034 , HIS A:3071 , ASN A:3104BINDING SITE FOR RESIDUE P6G A 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H84)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:2903 -Pro A:2904
2Gly A:3135 -Leu A:3136
3Ile B:2903 -Pro B:2904
4Gly B:3135 -Leu B:3136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H84)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PHOSPHOPANTETHEINEPS00012 Phosphopantetheine attachment site.PKS1_DICDI2931-2946
 
  2A:2931-2946
B:2931-2946

(-) Exons   (0, 0)

(no "Exon" information available for 2H84)

(-) 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:363
 aligned with PKS1_DICDI | Q55E72 from UniProtKB/Swiss-Prot  Length:3147

    Alignment length:363
                                  2794      2804      2814      2824      2834      2844      2854      2864      2874      2884      2894      2904      2914      2924      2934      2944      2954      2964      2974      2984      2994      3004      3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114      3124      3134      3144   
          PKS1_DICDI   2785 NNSFVLGIGISVPGEPISQQSLKDSISNDFSDKAETNEKVKRIFEQSQIKTRHLVRDYTKPENSIKFRHLETITDVNNQFKKVVPDLAQQACLRALKDWGGDKGDITHIVSVTSTGIIIPDVNFKLIDLLGLNKDVERVSLNLMGCLAGLSSLRTAASLAKASPRNRILVVCTEVCSLHFSNTDGGDQMVASSIFADGSAAYIIGCNPRIEETPLYEVMCSINRSFPNTENAMVWDLEKEGWNLGLDASIPIVIGSGIEAFVDTLLDKAKLQTSTAISAKDCEFLIHTGGKSILMNIENSLGIDPKQTKNTWDVYHAYGNMSSASVIFVMDHARKSKSLPTYSISLAFGPGLAFEGCFLKNVV 3147
               SCOP domains d2h84a1 A:2785-2998 automated matches                                                                                                                                                                                 d2h84a2 A:2999-3147 automated matches                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.....eehhhhhhhhhhhh..hhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhh....hhhhhhhhhhh..eeeeeeee..........eeeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhh............eeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eeeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHOPANTETHEI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2h84 A 2785 NNSFVLGIGISVPGEPISQQSLKDSISNDFSDKAETNEKVKRIFEQSQIKTRHLVRDYTKPENSIKFRHLETITDVNNQFKKVVPDLAQQACLRALKDWGGDKGDITHIVSVTSTGIIIPDVNFKLIDLLGLNKDVERVSLNLMGCLAGLSSLRTAASLAKASPRNRILVVCTEVCSLHFSNTDGGDQMVASSIFADGSAAYIIGCNPRIEETPLYEVMCSINRSFPNTENAMVWDLEKEGWNLGLDASIPIVIGSGIEAFVDTLLDKAKLQTSTAISAKDCEFLIHTGGKSILMNIENSLGIDPKQTKNTWDVYHAYGNMSSASVIFVMDHARKSKSLPTYSISLAFGPGLAFEGCFLKNVV 3147
                                  2794      2804      2814      2824      2834      2844      2854      2864      2874      2884      2894      2904      2914      2924      2934      2944      2954      2964      2974      2984      2994      3004      3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114      3124      3134      3144   

Chain B from PDB  Type:PROTEIN  Length:363
 aligned with PKS1_DICDI | Q55E72 from UniProtKB/Swiss-Prot  Length:3147

    Alignment length:363
                                  2794      2804      2814      2824      2834      2844      2854      2864      2874      2884      2894      2904      2914      2924      2934      2944      2954      2964      2974      2984      2994      3004      3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114      3124      3134      3144   
          PKS1_DICDI   2785 NNSFVLGIGISVPGEPISQQSLKDSISNDFSDKAETNEKVKRIFEQSQIKTRHLVRDYTKPENSIKFRHLETITDVNNQFKKVVPDLAQQACLRALKDWGGDKGDITHIVSVTSTGIIIPDVNFKLIDLLGLNKDVERVSLNLMGCLAGLSSLRTAASLAKASPRNRILVVCTEVCSLHFSNTDGGDQMVASSIFADGSAAYIIGCNPRIEETPLYEVMCSINRSFPNTENAMVWDLEKEGWNLGLDASIPIVIGSGIEAFVDTLLDKAKLQTSTAISAKDCEFLIHTGGKSILMNIENSLGIDPKQTKNTWDVYHAYGNMSSASVIFVMDHARKSKSLPTYSISLAFGPGLAFEGCFLKNVV 3147
               SCOP domains d2h84b1 B:2785-2998 automated matches                                                                                                                                                                                 d2h84b2 B:2999-3147 automated matches                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....eehhhhhhhhhhhh..hhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhhh....hhhhhhhhhhh..eeeeeeeee.........eeeeeeeeee.......eeeeee..eeeeee..hhhhhhhhhhhhhhhhhhhhhh.......hhhhheeee...hhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......eeeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHOPANTETHEI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2h84 B 2785 NNSFVLGIGISVPGEPISQQSLKDSISNDFSDKAETNEKVKRIFEQSQIKTRHLVRDYTKPENSIKFRHLETITDVNNQFKKVVPDLAQQACLRALKDWGGDKGDITHIVSVTSTGIIIPDVNFKLIDLLGLNKDVERVSLNLMGCLAGLSSLRTAASLAKASPRNRILVVCTEVCSLHFSNTDGGDQMVASSIFADGSAAYIIGCNPRIEETPLYEVMCSINRSFPNTENAMVWDLEKEGWNLGLDASIPIVIGSGIEAFVDTLLDKAKLQTSTAISAKDCEFLIHTGGKSILMNIENSLGIDPKQTKNTWDVYHAYGNMSSASVIFVMDHARKSKSLPTYSISLAFGPGLAFEGCFLKNVV 3147
                                  2794      2804      2814      2824      2834      2844      2854      2864      2874      2884      2894      2904      2914      2924      2934      2944      2954      2964      2974      2984      2994      3004      3014      3024      3034      3044      3054      3064      3074      3084      3094      3104      3114      3124      3134      3144   

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H84)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H84)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PKS1_DICDI | Q55E72)
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:0016210    naringenin-chalcone synthase activity    Catalysis of the reaction: 3 malonyl-CoA + 4-coumaroyl-CoA = 4 CoA + naringenin chalcone + 3 CO2.
    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:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    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).
biological process
    GO:0031152    aggregation involved in sorocarp development    The process whose specific outcome is the progression of the aggregate over time, from its formation to the point when a slug is formed. Aggregate development begins in response to starvation and continues by the chemoattractant-mediated movement of cells toward each other. The aggregate is a multicellular structure that gives rise to the slug.
    GO:0043327    chemotaxis to cAMP    The directed movement of a motile cell or organism in response to the presence of 3',5'-cAMP.
    GO:0009813    flavonoid biosynthetic process    The chemical reactions and pathways resulting in the formation of flavonoids, a group of phenolic derivatives containing a flavan skeleton.
    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.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    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.
    GO:0030639    polyketide biosynthetic process    The chemical reactions and pathways resulting in the formation of polyketides, any of a diverse group of natural products synthesized via linear poly-beta-ketones, which are themselves formed by repetitive head-to-tail addition of acetyl (or substituted acetyl) units indirectly derived from acetate (or a substituted acetate) by a mechanism similar to that for fatty acid biosynthesis but without the intermediate reductive steps.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0043949    regulation of cAMP-mediated signaling    Any process which modulates the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
    GO:0019505    resorcinol metabolic process    The chemical reactions and pathways involving resorcinol (C6H4(OH)2), a benzene derivative with many applications, including dyes, explosives, resins and as an antiseptic.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0048837    sorocarp sorus development    The process whose specific outcome is the progression of the sorocarp sorus over time, from its formation to the mature structure. A sorocarp sorus is the spore containing structure of a sorocarp.
    GO:0044671    sorocarp spore cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a sorocarp spore cell, a cell of the sorocarp sorus. A sorocarp is the fruiting body characteristic of certain cellular slime moulds (e.g., Dictyosteliida) and consists of both stalk and a sorus (spore mass).
    GO:0031149    sorocarp stalk cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a sorocarp stalk cell, any of the cellulose-covered cells that form the stalk of a sorocarp. An example of this process is found in Dictyostelium discoideum.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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