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(-) Description

Title :  CRYSTAL STRUCTURE OF EPOXIDE HYDROLASE FOR POLYETHER LASALOCID A BIOSYNTHESIS
 
Authors :  K. Hotta, I. I. Mathews, X. Chen, C. -Y. Kim
Date :  08 Apr 11  (Deposition) - 07 Mar 12  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Ntf2-Like, Epoxide-Opening Cyclic Ether Formation, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hotta, X. Chen, R. S. Paton, A. Minami, H. Li, K. Swaminathan, I. I. Mathews, K. Watanabe, H. Oikawa, K. N. Houk, C. -Y. Kim
Enzymatic Catalysis Of Anti-Baldwin Ring Closure In Polyether Biosynthesis
Nature V. 483 355 2012
PubMed-ID: 22388816  |  Reference-DOI: 10.1038/NATURE10865

(-) Compounds

Molecule 1 - EPOXIDE HYDROLASE
    Chains: A
    EC Number: 3.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LASB, LSD19
    Organism Scientific: STREPTOMYCES LASALIENSIS
    Organism Taxid: 324833

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric/Biological Unit (7, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FMT3Ligand/IonFORMIC ACID
3GOL2Ligand/IonGLYCEROL
4ILD1Ligand/Ion(4R,5S)-3-[(2R)-2-{(2S,2'R,4S,5S,5'R)-2,5'-DIETHYL-5'-[(1S)-1-HYDROXYETHYL]-4-METHYLOCTAHYDRO-2,2'-BIFURAN-5-YL}BUTANOYL]-4-METHYL-5-PHENYL-1,3-OXAZOLIDIN-2-ONE
5LSB1Ligand/Ion(4R,5S)-3-[(2R,3S,4S)-2-ETHYL-5-[(3R)-2-ETHYL-3-[2-[(2R,3R)-2-ETHYL-3-METHYL-OXIRAN-2-YL]ETHYL]OXIRAN-2-YL]-3-HYDROXY-4-METHYL-PENTANOYL]-4-METHYL-5-PHENYL-1,3-OXAZOLIDIN-2-ONE
6MOH2Ligand/IonMETHANOL
7NA1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:14 , CYS A:15 , ASP A:38 , LEU A:55 , GLU A:65 , LEU A:81 , VAL A:85 , VAL A:87 , THR A:100 , VAL A:102 , GLY A:104 , ILE A:106 , VAL A:119 , TRP A:121 , HOH A:435BINDING SITE FOR RESIDUE LSB A 301
02AC2SOFTWAREASP A:170 , TRP A:175 , ARG A:177 , HIS A:186 , MET A:189 , ALA A:190 , GLU A:197 , LEU A:228 , HIS A:231 , ILE A:249 , TYR A:251 , TRP A:270 , FMT A:310 , FMT A:311BINDING SITE FOR RESIDUE ILD A 302
03AC3SOFTWAREARG A:167 , GLU A:169 , THR A:176 , GLU A:265 , ARG A:267BINDING SITE FOR RESIDUE GOL A 303
04AC4SOFTWAREPRO A:39 , ARG A:131 , GLU A:136 , GLN A:206 , HOH A:423 , HOH A:486 , HOH A:515BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREARG A:35 , GLU A:116BINDING SITE FOR RESIDUE ACT A 305
06AC6SOFTWAREHIS A:74 , ASP A:152 , HIS A:231 , HIS A:232BINDING SITE FOR RESIDUE ACT A 306
07AC7SOFTWAREGLU A:137 , LYS A:140 , THR A:202 , HOH A:417BINDING SITE FOR RESIDUE FMT A 309
08AC8SOFTWAREHIS A:146 , ILE A:150 , HIS A:186 , ALA A:190 , GLU A:197 , ILD A:302BINDING SITE FOR RESIDUE FMT A 310
09AC9SOFTWAREARG A:177 , HIS A:186 , THR A:198 , ILD A:302 , HOH A:449 , HOH A:461 , HOH A:495BINDING SITE FOR RESIDUE FMT A 311
10BC1SOFTWAREVAL A:123 , SER A:126 , THR A:129 , HOH A:447 , HOH A:452BINDING SITE FOR RESIDUE NA A 312

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:38 -Pro A:39
2Asp A:170 -Pro A:171
3Leu A:222 -Pro A:223
4Asp A:279 -Pro A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RGA)

(-) 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:281
 aligned with LSD19_STRLS | B6ZK72 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:281
                             1                                                                                                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279 
          LSD19_STRLS     - -MPAETVRKEVALEYCRRVNAGELEGVLQLFAPDALLVDPLGTEPVVGRAALAARLAPALRGAVHEEPGRPYAAHDGTSVVLPATVTVGAPGAPPQRRGRTRVMGVIEVGEDGLIREMRVMWGVTDSSWTARPAPDEERRKELAREHCLRINDGDVDGLLKLYSPRIRFEDPVGSWTRTGLEALRAHATMAVGSNVRETAGLTVAGQDGRHAAVTVSATMDYLPSGPLLARHHLMTLPAPADPHRALIGIEYVMVIGVDADGLIDEMRAYWGATDVSLLDP 280
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee.......eehhhhhhhhhhhhhhh..eeee..........eeeeeeeeee.....hhhhheeeeeeeeeee.....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eeehhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeeeee..hhhhhhhhh..............eeeeeeeeeeee.....eeeeeee.hhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rga A   0 HMPAETVRKEVALEYCRRVNAGELEGVLQLFAPDARLVDPLGTEPVVGRAALAARLAPALRGAVHEEPGRPYAAHDGTSVVLPATVTVGAPGAPPQRRGRTRVMGVIEVGEDGLIREMRVMWGVTDSSWTARPAPDEERRKELAREHCLRINDGDVDGLLKLYSPRIRFEDPVGSWTRTGLEALRAHATMAVGSNVRETAGLTVAGQDGRHAAVTVSATMDYLPSGPLLARHHLMTLPAPADPHRALIGIEYVMVIGVDADGLIDEMRAYWGATDVSLLDP 280
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
   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 3RGA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LSD19_STRLS | B6ZK72)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
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.

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