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(-) Description

Title :  ENTF, A TERMINAL NONRIBOSOMAL PEPTIDE SYNTHETASE MODULE BOUND TO THE MBTH-LIKE PROTEIN YBDZ
 
Authors :  B. R. Miller, A. M. Gulick
Date :  11 Apr 16  (Deposition) - 14 Sep 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nonribosomal Peptide Synthetase, Nrps, Condensation, Adenylation, Pcp, Thioesterase, Mbth-Like Protein, Phosphopantetheine, Biosynthetic Protein, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Miller, E. J. Drake, C. Shi, C. C. Aldrich, A. M. Gulick
Structures Of A Nonribosomal Peptide Synthetase Module Boun To Mbth-Like Proteins Support A Highly Dynamic Domain Architecture.
J. Biol. Chem. V. 291 22559 2016
PubMed-ID: 27597544  |  Reference-DOI: 10.1074/JBC.M116.746297
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENTEROBACTIN SYNTHASE COMPONENT F
    Chains: A
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMIS
    Gene: ENTF, B0586, JW0578
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: ENTEROCHELIN SYNTHASE F,SERINE-ACTIVATING ENZYME,SERYL-AMP LIGASE
    Variant: W3110
 
Molecule 2 - ENTEROBACTIN BIOSYNTHESIS PROTEIN YBDZ
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YBDZ, B4511, JW0577
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Variant: W3110

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
175C1Ligand/Ion5'-({[(2R,3S)-3-AMINO-4-HYDROXY-2-{[2-({N-[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]-BETA-ALANYL}AMINO)ETHYL]SULFANYL}BUTYL]SULFONYL}AMINO)-5'-DEOXYADENOSINE
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:647 , ASP A:648 , ARG A:673 , VAL A:693 , SER A:722 , GLY A:723 , GLU A:724 , ALA A:725 , ASN A:744 , LEU A:745 , TYR A:746 , GLY A:747 , PRO A:748 , THR A:749 , VAL A:753 , ASP A:754 , ILE A:775 , ASP A:840 , TYR A:852 , ARG A:855 , LYS A:861 , ARG A:863 , GLY A:864 , GLN A:865 , ARG A:866 , SER A:1006 , HOH A:1420binding site for residue 75C A 1301
2AC2SOFTWARELYS A:861 , ARG A:903binding site for residue CL A 1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JA1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:288 -Pro A:289
2Arg A:1101 -Pro A:1102
3Gly A:1130 -Pro A:1131
4Arg A:1154 -Gly A:1155

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JA1)

(-) Exons   (0, 0)

(no "Exon" information available for 5JA1)

(-) 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:1231
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeee...hhhhhhhhhhhhhhhh....eee...eee...........ee.....hhhhhhhhhhhhhhh...........eee..ee....eeeeeeeee.......hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....................eeeeeee..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeeeee...hhhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhh....hhhhhhhh.........eeee.............eeeeeeee......eeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.........hhhhhhhhhhhhh...eeee....eeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhh....eee....................eeeeeee.......eeeeeehhhhhhhhhhhhhhh......eeee.......hhhhhhhhhhh...eeee.......hhhhhhhhhhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhh.eeee.....hhhhhhhhhhhh...eeeee.hhhhh...eeee.hhhhhhh.........ee...eee...............eeeeeee.....eee.hhhhhhhheee.......eeeeeeeeeee.....eeeeee...eeee..eeeehhhhhhhhh......eeeeeee..hhhhh......eeeeeee.......hhhhhhhhhh...hhhhh..eeee.............................hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhh.....eeeee.....eeeee......hhhhhhhhhhh....eeeee......hhhhhh.hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhh......eeeeeee..........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.......eeeeeee....hhhhhhhhh.eeeeeee...........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ja1 A   21 SELPSAWSVAHYVELTGEVDSPLLARAVVAGLAQADTLRMRFTVWQWVDDALTFELPEIIDLRTNIDPHGTAQALMQADLQQDLRVDSGKPLVFHQLIQVADNRWYWYQRYHHLLVDGFSFPAITRQIANIYCTWLRGEPTPASPFTPFADVVEEYQQYRESEAWQRDAAFWAEQRRQLPPPASLSPAPLPGRSASADILRLKLEFTDGEFRQLATQLSGVQRTDLALALAALWLGRLCNRMDYAAGFIFMRRLGSAALTATGPVLNVLPLGIHIAAQETLPELATRLAAQLKKMRRHQRYDAEQIVRDSAGDEPLFGPVLNIKVFDYQLDIPDVQAQTHTLATGPVNDLELALFPDVHGDLSIEILANKQRYDEPTLIQHAERLKMLIAQFAADPALLCGDVDIMLPGEYAQLAQLNATQVEIPETTLSALVAEQAAKTPDAPALADARYLFSYREMREQVVALANLLRERGVKPGDSVAVALPRSVFLTLALHAIVEAGAAWLPLDTGYPDDRLKMMLEDARPSLLITTDDQLPRFSDVPNLTSLCYNAPLTPQGSAPLQLSQPHHTAYIIFTSGSTGRPKGVMVGQTAIVNRLLWMQNHYPLTGEDVVAQKTPCSFDVSVWEFFWPFIAGAKLVMAEPEAHRDPLAMQQFFAEYGVTTTHFVPSMLAAFVASLTPQTARQSCATLKQVFCSGEALPADLCREWQQLTGAPLHNLYGPTEAAVDVSWYPAFGEELAQVRGSSVPIGYPVWNTGLRILDAMMHPVPPGVAGDLYLTGIQLAQGYLGRPDLTASRFIADPFAPGERMYRTGDVARWLDNGAVEYLGRSDDQLKIRGQRIELGEIDRVMQALPDVEQAVTHACVINQAAATGGDARQLVGYLVSQSGLPLDTSALQAQLRETLPPHMVPVVLLQLPQLPLSANGKLDRKALPLPELRAPKAGSETIIAAAFSSLLGCDVQDADADFFALGGHSLLAMKLAAQLSRQVARQVTPGQVMVASTVAKLATIMGFETILPLREGNGPTLFCFHPASGFAWQFSVLSRYLDPQWSIIGIQSPRPNGPMQTAANLDEVCEAHLATLLEQQPHGPYYLLGYSLGGTLAQGIAARLRARGEQVAFLGLLDTWPPETLDPEVLAEINREREAFLAAQQGSTELFTTIEGNYADAVRLLTTAHSVPFDGKATLFVAERTSPERAWSPWIAELDIYRQDCAHVDIISPGTFEKIGPIIRATLN 1292
                                    30        40        50        60  ||    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335|      348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958    || 974       984       994      1004      1014      1024      1034      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1184      1194      1204||    1216      1226      1236      1251      1261      1271      1281      1291 
                                                                     63|                                                                                                                                                                                                                                                                       335|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             963|                                                                   1041|                                                                                                                   1171|                   1205|                                1244|                                          
                                                                      69                                                                                                                                                                                                                                                                        339                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              970                                                                    1052                                                                                                                    1182                    1208                                 1250                                          


Chain B from PDB  Type:PROTEIN  Length:66
                                                                                                   
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh....eeeee.....eeeee.........eeeeeeehhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                5ja1 B    3 FSNPFDDPQGAFYILRNAQGQFSLWPQQCVLPAGWDIVCQPQSQASCQQWLEAHWRTLTPTNFTQL   68
                                    12        22        32        42        52        62
   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 5JA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JA1)

(-) Gene Ontology  (16, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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    Arg A:1101 - Pro A:1102   [ RasMol ]  
    Arg A:1154 - Gly A:1155   [ RasMol ]  
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    Gly A:288 - Pro A:289   [ RasMol ]  
 

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  5ja1
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENTF_ECOLI | P11454: 2roq 3tej 5ja2 5t3d

(-) Related Entries Specified in the PDB File

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