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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ERYTHROMYCIN DEHYDRATASE
 
Authors :  A. T. Keatinge-Clay
Date :  20 Sep 08  (Deposition) - 11 Nov 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dehydratase Double Hotdog Fold Cis-Proline, Acyltransferase, Antibiotic Biosynthesis, Multifunctional Enzyme, Nadp, Phosphopantetheine, Transferase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Keatinge-Clay
Crystal Structure Of The Erythromycin Polyketide Synthase Dehydratase.
J. Mol. Biol. V. 384 941 2008
PubMed-ID: 18952099  |  Reference-DOI: 10.1016/J.JMB.2008.09.084
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERYTHROMYCIN DEHYDRATASE
    ChainsA
    EC Number4.2.1.61
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET
    FragmentERYDH4 (UNP RESIDUES 2362 TO 2653)
    GeneERYA
    Organism ScientificSACCHAROPOLYSPORA ERYTHRAEA
    Organism Taxid1836
    SynonymORF 2, 6-DEOXYERYTHRONOLIDE B SYNTHASE II, DEBS 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:243 , HOH A:456 , HOH A:491BINDING SITE FOR RESIDUE SO4 A 289
2AC2SOFTWAREARG A:8 , ASP A:20 , ARG A:92 , HOH A:324BINDING SITE FOR RESIDUE CL A 290

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EL6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:144 -Pro A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EL6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EL6)

(-) Exons   (0, 0)

(no "Exon" information available for 3EL6)

(-) Sequences/Alignments

Asymmetric 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:271
 aligned with ERYA2_SACER | Q03132 from UniProtKB/Swiss-Prot  Length:3567

    Alignment length:275
                                  2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495      2505      2515      2525      2535      2545      2555      2565      2575      2585      2595      2605      2615      2625      2635     
         ERYA2_SACER   2366 DVSALGVRGAEHPLLLAAVDVPGHGGAVFTGRLSTDEQPWLAEHVVGGRTLVPGSVLVDLALAAGEDVGLPVLEELVLQRPLVLAGAGALLRMSVGAPDESGRRTIDVHAAEDVADLADAQWSQHATGTLAQGVAAGPRDTEQWPPEDAVRIPLDDHYDGLAEQGYEYGPSFQALRAAWRKDDSVYAEVSIAADEEGYAFHPVLLDAVAQTLSLGALGEPGGGKLPFAWNTVTLHASGATSVRVVATPAGADAMALRVTDPAGHLVATVDSLVVR 2640
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.ee.....eeeeee......eeeeeee....hhhhh.eee..ee..hhhhhhhhhhhhhhhhh..eeeeeee..........eeeeeeeeee.....eeeeeeeee...hhhhh..eeeeeeeee..................ee....hhhhhhhhh.eee.hhhh.eeeeeee..eeeeeee..........hhhhhhhhhhhhhhh....----.eeeeeeeeee......eeeeeeee....eeeeeee.....eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3el6 A    1 DVSALGVRGAEHPLLLAAVDVPGHGGAVFTGRLSTDEQPWLAEHVVGGRTLVPGSVLVDLALAAGEDVGLPVLEELVLQRPLVLAGAGALLRMSVGAPDESGRRTIDVHAAEDVADLADAQWSQHATGTLAQGVAAGPRDTEQWPPEDAVRIPLDDHYDGLAEQGYEYGPSFQALRAAWRKDDSVYAEVSIAADEEGYAFHPVLLDAVAQTLSLGALGE----KLPFAWNTVTLHASGATSVRVVATPAGADAMALRVTDPAGHLVATVDSLVVR  275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        |-   |   230       240       250       260       270     
                                                                                                                                                                                                                                                    219  224                                                   

   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 3EL6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EL6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EL6)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (ERYA2_SACER | Q03132)
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:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0047879    erythronolide synthase activity    Catalysis of the reaction: 6 malonyl-CoA + propionyl-CoA = 7 CoA + 6-deoxyerythronolide B.
    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:0031177    phosphopantetheine binding    Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
    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: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:0033068    macrolide biosynthetic process    The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ERYA2_SACER | Q031321pzq 1pzr 2qo3

(-) Related Entries Specified in the PDB File

2fr0 KETOREDUCTASE FROM MODULE 1 OF THE ERYTHROMYCIN POLYKETIDE SYNTHASE
2hg4 KETOSYNTHASE+ACYLTRANSFERASE DIDOMAIN FROM MODULE 5 OF THE ERYTHROMYCIN POLYKETIDE SYNTHASE