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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THIOESTERASE DOMAIN OF DEOXYERYTHRONOLIDE B SYNTHASE
 
Authors :  F. Bergeret, P. Argyropoulos, C. N. Boddy, T. M. Schmeing
Date :  06 Aug 15  (Deposition) - 09 Dec 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Thioesterase Domaine Alpha / Beta Hydrolase Fold Deoxyerythronolide B Synthase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Argyropoulos, F. Bergeret, C. Pardin, J. M. Reimer, A. Pinto, C. N. Boddy, T. M. Schmeing
Towards A Characterization Of The Structural Determinants O Specificity In The Macrocyclizing Thioesterase For Deoxyerythronolide B Biosynthesis.
Biochim. Biophys. Acta V. 1860 486 2015
PubMed-ID: 26592346  |  Reference-DOI: 10.1016/J.BBAGEN.2015.11.007

(-) Compounds

Molecule 1 - ERYTHRONOLIDE SYNTHASE, MODULES 5 AND 6
    Chains: A
    EC Number: 2.3.1.94
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBACP
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 2904-3172
    Gene: ERYA
    Organism Scientific: SACCHAROPOLYSPORA ERYTHRAEA
    Organism Taxid: 1836
    Synonym: 6-DEOXYERYTHRONOLIDE B SYNTHASE III,DEBS 3,ORF 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2CA3Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:83 , ARG A:87 , HIS A:141 , THR A:195 , HOH A:406 , HOH A:536 , HOH A:550 , HOH A:566binding site for residue 1PE A 301
2AC2SOFTWARETYR A:22 , VAL A:31 , GLN A:176 , MET A:179 , LEU A:183 , THR A:187 , ASP A:210 , THR A:213 , GLY A:214binding site for residue 1PE A 302
3AC3SOFTWAREVAL A:27 , ASP A:49 , HOH A:411 , HOH A:568binding site for residue CA A 303
4AC4SOFTWAREGLU A:108 , ASP A:199 , HOH A:500binding site for residue CA A 304
5AC5SOFTWAREASP A:275 , HOH A:446 , HOH A:459 , HOH A:469binding site for residue CA A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5D3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D3K)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5D3K)

(-) 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:269
                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhh...ee..........eeee......eeeee.......hhhhhhhhhhhhh....eeee..........ee.hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh........eeeeee....................eeeee....hhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d3k A  15 SSALRDGYRQAGVSGRVRSYLDLLAGLSDFREHFDGSDGFSLDLVDMADGPGEVTVICCAGTAAISGPHEFTRLAGALRGIAPVRAVPQPGYEEGEPLPSSMAAVAAVQADAVIRTQGDKPFVVAGHSAGALMAYALATELLDRGHPPRGVVLIDVYPPGHQDAMNAWLEELTATLFDRETVRMDDTRLTALGAYDRLTGQWRPRETGLPTLLVSAGEPMGPWPDDSWKPTWPFEHDTVAVPGDHFTMVQEHADAIARHIDAWLGGGNS 283
                                    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
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  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 5D3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D3K)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        ERYA3_SACER | Q03133: 1kez 1mo2 1pzr 2hg4 5d3z

(-) Related Entries Specified in the PDB File

5d2r