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(-) Description

Title :  PROTEIN COMPLEX OF A-STATE TYCC3-APO-PCP WITH THE PPTASE SFP (MODEL)
 
Authors :  A. Koglin, M. -M. Blum, V. V. Rogov, M. A. Marahiel, F. Bernhard, V. Doetsch
Date :  17 Mar 06  (Deposition) - 01 Aug 06  (Release) - 01 Aug 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B
Keywords :  4'-Phosphopantetheinyl Transferase Sfp/Coenzyme A In Complex With A-State Tycc3-Apo-Pcp, Coenzyme A (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Koglin, M. R. Mofid, F. Loehr, B. Schaefer, V. V. Rogov, M. -M. Blum, T. Mittag, M. A. Marahiel, F. Bernhard, V. Doetsch
Conformational Switches Modulate Protein Interactions In Peptide Antibiotic Synthetases
Science V. 312 273 2006
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4'-PHOSPHOPANTETHEINYL TRANSFERASE SFP
    ChainsA
    EC Number2.7.8.-
    GenusSFP, LPA-8
    Organism CommonBACTERIA
    Organism ScientificBACILLUS SUBTILIS
    StrainATCC 21332
    SynonymSURFACTIN SYNTHETASE-ACTIVATING ENZYME
 
Molecule 2 - TYROCIDINE SYNTHETASE III
    ChainsB
    FragmentACYL CARRIER 3, TYCC3 THIOESTER DOMAIN
    GenusTYCC
    MutationYES
    Organism CommonBACTERIA
    Organism ScientificBREVIBACILLUS PARABREVIS
    StrainATCC 8185
    SynonymNON-RIBOSOMAL PEPTIDE SYNTHETASE PEPTIDYL CARRIER PROTEIN

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (2, 2)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 2GE1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GE1)

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Leu A:182 -Pro A:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Theoretical Model (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SFP_BACSU_001 *S22TSFP_BACSU  ---  ---AT22T
2UniProtVAR_SFP_BACSU_002 *C97GSFP_BACSU  ---  ---AG97G
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARRIERPS50075 Carrier protein (CP) domain profile.TYCC_BREPA965-1040
2002-2077
3040-3115
4075-4150
5119-5194
6162-6237
  1-
-
B:10-83
-
-
-
2PHOSPHOPANTETHEINEPS00012 Phosphopantetheine attachment site.TYCC_BREPA995-1010
2032-2047
3070-3085
4105-4120
5149-5164
6192-6207
  1-
-
B:40-55
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 2GE1)

(-) Sequences/Alignments

Theoretical Model
   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:228
 aligned with SFP_BACSU | P39135 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:228
                                                                                                                                                                                                                                                         224    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   |    
           SFP_BACSU      1 MKIYGIYMDRPLSQEENERFMSFISPEKREKCRRFYHKEDAHRTLLGDVLVRSVISRQYQLDKSDIRFSTQEYGKPCIPDLPDAHFNISHSGRWVICAFDSQPIGIDIEKTKPISLEIAKRFFSKTEYSDLLAKDKDEQTDYFYHLWSMKESFIKQEGKGLSLPLDSFSVRLHQDGQVSIELPDSHSPCYIKTYEVDPGYKMAVCAAHPDFPEDITMVSYEELL----    -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhh..ee.....ee.......eeeeeee..eeeeeee....eeeeee....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeee.hhh.eeee........eeeee.....eeeeeee.........ee.hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------T--------------------------------------------------------------------------G----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2ge1 A    1 MKIYGIYMDRPLSQEENERFMTFISPEKREKCRRFYHKEDAHRTLLGDVLVRSVISRQYQLDKSDIRFSTQEYGKPCIPDLPDAHFNISHSGRWVIGAFDSQPIGIDIEKTKPISLEIAKRFFSKTEYSDLLAKDKDEQTDYFYHLWSMKESFIKQEGKGLSLPLDSFSVRLHQDGQVSIELPDSHSPCYIKTYEVDPGYKMAVCAAHPDFPEDITMVSYEELLRAAA  228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with TYCC_BREPA | O30409 from UniProtKB/Swiss-Prot  Length:6486

    Alignment length:82
                                  3043      3053      3063      3073      3083      3093      3103      3113  
          TYCC_BREPA   3034 TEAQYVAPTNAVESKLAEIWERVLGVSGIGILDNFFQIGGHSLKAMAVAAQVHREYQVELPLKVLFAQPTIKALAQYVATSG 3115
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhh.............................hhhhhhhhh............hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------CARRIER  PDB: B:10-83 UniProt: 3040-3115                                     PROSITE (1)
                PROSITE (2) ------------------------------------PHOSPHOPANTETHEI------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                2ge1 B    4 TEAQYVAPTNAVESKLAEIWERVLGVSGIGILDNFFQIGGHSLKAMAVAAQVHREYQVELPLKVLFAQPTIKALAQYVATRS   85
                                    13        23        33        43        53        63        73        83  

   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  (0, 0)

(no "SCOP Domain" information available for 2GE1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GE1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GE1)

(-) Gene Ontology  (14, 15)

Theoretical Model(hide GO term definitions)
Chain A   (SFP_BACSU | P39135)
molecular function
    GO:0008897    holo-[acyl-carrier-protein] synthase activity    Catalysis of the reaction: CoA + substrate-serine = adenosine 3',5'-bisphosphate + substrate-serine-4'-phosphopantetheine. The transfer of the 4'-phosphopantetheine (Ppant) co-factor from coenzyme A to the hydroxyl side chain of the serine residue of acyl- or peptidyl-carrier protein (ACP or PCP) to convert them from the apo to the holo form.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0019878    lysine biosynthetic process via aminoadipic acid    The chemical reactions and pathways resulting in the formation of lysine by the aminoadipic pathway.
    GO:1900192    positive regulation of single-species biofilm formation    Any process that activates or increases the frequency, rate or extent of single-species biofilm formation.

Chain B   (TYCC_BREPA | O30409)
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:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        SFP_BACSU | P391351qr0 2ge0 4mrt
        TYCC_BREPA | O304091dny 2gdw 2gdx 2gdy 2jgp 2k2q 2md9 4mrt

(-) Related Entries Specified in the PDB File

1qr0 CRYSTAL STRUCTURE OF SFP
2gdw SOLUTION STRUCTURE OF THE B. BREVIS TYCC3-PCP IN A/H-STATE
2gdx SOLUTION STRUCTURE OF THE B. BREVIS TYCC3-PCP IN H-STATE
2gdy SOLUTION STRUCTURE OF THE B. BREVIS TYCC3-PCP IN A-STATE
2geo ACTIVE COMPLEX OF COENZYME A AND THE PPTASE SFP FROM B. SUBTILIS