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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TWO-DOMAIN NON-RIBOSOMAL PEPTIDE SYNTHETASE ENTB CONTAINING ISOCHORISMATE LYASE AND ARYL-CARRIER PROTEIN DOMAINS
 
Authors :  E. J. Drake, D. A. Nicolai, A. M. Gulick
Date :  17 Jan 06  (Deposition) - 02 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Entb, Nrps, Multi-Domain, Acp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. J. Drake, D. A. Nicolai, A. M. Gulick
Structure Of The Entb Multidomain Nonribosomal Peptide Synthetase And Functional Analysis Of Its Interaction With The Ente Adenylation Domain.
Chem. Biol. V. 13 409 2006
PubMed-ID: 16632253  |  Reference-DOI: 10.1016/J.CHEMBIOL.2006.02.005

(-) Compounds

Molecule 1 - ISOCHORISMATASE
    ChainsA, B
    EC Number3.3.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPRF7
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePET15BTEV
    GeneENTB, ENTG
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    StrainJM109
    SynonymISOCHORISMATE LYASE, 2,3 DIHYDRO-2,3 DIHYDROXYBENZOATE SYNTHASE, ENTEROBACTIN SYNTHETASE COMPONENT B, ENTEROCHELIN SYNTHASE B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MG8Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:240 , HOH A:1095 , GLN B:69 , HOH B:1043BINDING SITE FOR RESIDUE MG B 991
02AC2SOFTWAREGLU A:185 , HOH B:1055 , HOH B:1056BINDING SITE FOR RESIDUE MG A 992
03AC3SOFTWAREASP A:110BINDING SITE FOR RESIDUE MG A 993
04AC4SOFTWAREASP B:110 , HOH B:1047 , HOH B:1052 , HOH B:1100BINDING SITE FOR RESIDUE MG B 994
05AC5SOFTWAREHIS B:15 , HOH B:1008 , HOH B:1103BINDING SITE FOR RESIDUE MG B 995
06AC6SOFTWAREHOH A:1016BINDING SITE FOR RESIDUE MG A 996
07AC7SOFTWAREASP A:227 , GLY A:242 , ASP A:244 , HOH A:1056 , HOH A:1067BINDING SITE FOR RESIDUE MG A 997
08AC8SOFTWAREGLN A:69 , HOH A:1057 , HOH A:1058 , HOH A:1111 , GLU B:228 , ASP B:240BINDING SITE FOR RESIDUE MG A 998
09AC9SOFTWARETYR B:152 , ILE B:155 , GLY B:156BINDING SITE FOR RESIDUE CL B 950
10BC1SOFTWARETYR A:152 , ILE A:155 , GLY A:156BINDING SITE FOR RESIDUE CL A 951
11BC2SOFTWARETHR A:159 , TYR A:192 , THR B:159 , THR B:162 , TYR B:192BINDING SITE FOR RESIDUE EDO A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FQ1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:151 -Tyr A:152
2Pro B:4 -Lys B:5
3Val B:151 -Tyr B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FQ1)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARRIERPS50075 Carrier protein (CP) domain profile.ENTB_ECOLI209-284
 
  2A:209-283
B:209-282

(-) Exons   (0, 0)

(no "Exon" information available for 2FQ1)

(-) 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:279
 aligned with ENTB_ECOLI | P0ADI4 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:279
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274         
           ENTB_ECOLI     5 KLQAYALPESHDIPQNKVDWAFEPQRAALLIHDMQDYFVSFWGENCPMMEQVIANIAALRDYCKQHNIPVYYTAQPKEQSDEDRALLNDMWGPGLTRSPEQQKVVDRLTPDADDTVLVKWRYSAFHRSPLEQMLKESGRNQLIITGVYAHIGCMTTATDAFMRDIKPFMVADALADFSRDEHLMSLKYVAGRSGRVVMTEELLPAPIPASKAALREVILPLLDESDEPFDDDNLIDYGLDSVRMMALAARWRKVHGDIDFVMLAKNPTIDAWWKLLSRE 283
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2fq1A01 A:5-207  [code=3.40.50.850, no name defined]                                                                                                                                                       ---------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh.........hhh.eeeeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....eeee..........hhhhhhhhh...eeeeeee...hhhhhhhhhhhhh..eeeeeeeeee..hhhhhhhhhhhhhhhh.eeehhhhhh......hhhhhhhhhhhhh...........hhhhh...hhhhhhhhhhh......hhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARRIER  PDB: A:209-283 UniProt: 209-284                                    PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fq1 A   5 KLQAYALPESHDIPQNKVDWAFEPQRAALLIHDMQDYFVSFWGENCPMMEQVIANIAALRDYCKQHNIPVYYTAQPKEQSDEDRALLNDMWGPGLTRSPEQQKVVDRLTPDADDTVLVKWRYSAFHRSPLEQMLKESGRNQLIITGVYAHIGCMTTATDAFMRDIKPFMVADALADFSRDEHLMSLKYVAGRSGRVVMTEELLPAPIPASKAALREVILPLLDESDEPFDDDNLIDYGLDSVRMMALAARWRKVHGDIDFVMLAKNPTIDAWWKLLSRE 283
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274         

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with ENTB_ECOLI | P0ADI4 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:279
                                    13        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         
           ENTB_ECOLI     4 PKLQAYALPESHDIPQNKVDWAFEPQRAALLIHDMQDYFVSFWGENCPMMEQVIANIAALRDYCKQHNIPVYYTAQPKEQSDEDRALLNDMWGPGLTRSPEQQKVVDRLTPDADDTVLVKWRYSAFHRSPLEQMLKESGRNQLIITGVYAHIGCMTTATDAFMRDIKPFMVADALADFSRDEHLMSLKYVAGRSGRVVMTEELLPAPIPASKAALREVILPLLDESDEPFDDDNLIDYGLDSVRMMALAARWRKVHGDIDFVMLAKNPTIDAWWKLLSR 282
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2fq1B01 B:4-207  [code=3.40.50.850, no name defined]                                                                                                                                                        --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh.........hhh.eeeeee..hhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhh.....eeee..........hhhhhhhhh...eeeeee....hhhhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhh.eeehhhhhh......hhhhhhhhhhhhh...................hhhhhhhhhhh......hhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CARRIER  PDB: B:209-282 UniProt: 209-284                                   PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fq1 B   4 PKLQAYALPESHDIPQNKVDWAFEPQRAALLIHDMQDYFVSFWGENCPMMEQVIANIAALRDYCKQHNIPVYYTAQPKEQSDEDRALLNDMWGPGLTRSPEQQKVVDRLTPDADDTVLVKWRYSAFHRSPLEQMLKESGRNQLIITGVYAHIGCMTTATDAFMRDIKPFMVADALADFSRDEHLMSLKYVAGRSGRVVMTEELLPAPIPASKAALREVILPLLDESDEPFDDDNLIDYGLDSVRMMALAARWRKVHGDIDFVMLAKNPTIDAWWKLLSR 282
                                    13        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         

   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 2FQ1)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FQ1)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ENTB_ECOLI | P0ADI4)
molecular function
    GO:0047527    2,3-dihydroxybenzoate-serine ligase activity    Catalysis of the reaction: ATP + 2,3-dihydroxybenzoate + L-serine = products of ATP breakdown + N-(2,3-dihydroxybenzoyl)-L-serine.
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008908    isochorismatase activity    Catalysis of the reaction: H(2)O + isochorismate = 2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate.
    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: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:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0009239    enterobactin biosynthetic process    The chemical reactions and pathways resulting in the formation of enterobactin, a catechol-derived siderochrome of Enterobacteria; enterobactin (N',N',N''-(2,6,10-trioxo-1,5,9-triacyclodecane-3,7,11-triyl)tris(2,3-dihydroxy)benzamide) is a self-triester of 2,3-dihydroxy-N-benzoyl-L-serine and a product of the shikimate pathway.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ENTB_ECOLI | P0ADI43rg2 4iz6

(-) Related Entries Specified in the PDB File

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