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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LSD19-LASALOCID A COMPLEX
 
Authors :  I. I. Mathews, K. Hotta, X. Chen, C. -Y. Kim
Date :  22 Dec 14  (Deposition) - 21 Jan 15  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Ntf2-Like Fold, Epoxide-Opening Cyclic Ether Formation, Isomerization, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. T. Wong, K. Hotta, X. Chen, M. Fang, K. Watanabe, C. Y. Kim
Epoxide Hydrolase-Lasalocid A Structure Provides Mechanisti Insight Into Polyether Natural Product Biosynthesis.
J. Am. Chem. Soc. V. 137 86 2015
PubMed-ID: 25535803  |  Reference-DOI: 10.1021/JA511374K

(-) Compounds

Molecule 1 - EPOXIDE HYDROLASE LASB
    Chains: A, B
    EC Number: 5.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCOLD1
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LASB, LSD19
    Organism Scientific: STREPTOMYCES LASALIENSIS
    Organism Taxid: 324833
    Synonym: LASALOCID BIOSYNTHESIS PROTEIN LSD19

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric Unit (5, 16)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FMT8Ligand/IonFORMIC ACID
3GOL2Ligand/IonGLYCEROL
4LSD2Ligand/IonLASALOCID A
5NA3Ligand/IonSODIUM ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT3Ligand/IonFORMIC ACID
3GOL1Ligand/IonGLYCEROL
4LSD1Ligand/IonLASALOCID A
5NA-1Ligand/IonSODIUM ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT5Ligand/IonFORMIC ACID
3GOL1Ligand/IonGLYCEROL
4LSD1Ligand/IonLASALOCID A
5NA-1Ligand/IonSODIUM ION
Biological Unit 3 (3, 24)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FMT16Ligand/IonFORMIC ACID
3GOL4Ligand/IonGLYCEROL
4LSD4Ligand/IonLASALOCID A
5NA-1Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:170 , SER A:174 , TRP A:175 , ARG A:177 , HIS A:186 , SER A:224 , HIS A:231 , TYR A:251 , TRP A:270 , HOH A:437 , HIS B:232 , HOH B:452BINDING SITE FOR RESIDUE LSD A 301
02AC2SOFTWAREHIS A:146 , ASP A:170 , GLU A:197 , TYR A:251 , MET A:253 , MET A:266BINDING SITE FOR RESIDUE GOL A 302
03AC3SOFTWAREGLU A:65 , LEU A:81BINDING SITE FOR RESIDUE FMT A 303
04AC4SOFTWARETYR A:14 , ASP A:38 , GLU A:65BINDING SITE FOR RESIDUE FMT A 304
05AC5SOFTWAREASP A:38BINDING SITE FOR RESIDUE FMT A 305
06AC6SOFTWAREVAL A:123 , SER A:126 , THR A:129 , HOH A:449 , HOH A:451BINDING SITE FOR RESIDUE NA A 306
07AC7SOFTWAREHIS A:232 , ASP B:170 , SER B:174 , TRP B:175 , ARG B:177 , HIS B:186 , SER B:224 , LEU B:228 , HIS B:231 , LEU B:233 , TYR B:251 , HOH B:422BINDING SITE FOR RESIDUE LSD B 301
08AC8SOFTWAREHIS B:146 , ASP B:170 , GLU B:197 , TYR B:251 , MET B:253 , MET B:266BINDING SITE FOR RESIDUE GOL B 302
09AC9SOFTWARETHR B:198 , GLY B:200 , THR B:214 , SER B:216 , HOH B:423BINDING SITE FOR RESIDUE FMT B 303
10BC1SOFTWAREHIS B:0 , GLU B:110BINDING SITE FOR RESIDUE FMT B 304
11BC2SOFTWAREGLU B:65 , LEU B:81BINDING SITE FOR RESIDUE FMT B 305
12BC3SOFTWAREHIS A:74 , HIS B:232 , ALA B:272 , NA B:308 , HOH B:420 , HOH B:429BINDING SITE FOR RESIDUE FMT B 306
13BC4SOFTWAREHIS A:232 , HIS B:74 , NA B:308 , HOH B:419 , HOH B:439BINDING SITE FOR RESIDUE FMT B 307
14BC5SOFTWAREHIS A:232 , HIS B:232 , FMT B:306 , FMT B:307BINDING SITE FOR RESIDUE NA B 308
15BC6SOFTWAREVAL B:123 , SER B:126 , THR B:129 , HOH B:465 , HOH B:466BINDING SITE FOR RESIDUE NA B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RZM)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric 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
5Asp B:38 -Pro B:39
6Asp B:170 -Pro B:171
7Leu B:222 -Pro B:223
8Asp B:279 -Pro B:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RZM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RZM)

(-) Exons   (0, 0)

(no "Exon" information available for 4RZM)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhhhh..eeee..........eeeeeeeee...eeeeeeeeee.....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhh.eeeeeeee.......eehhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhh..............eeeeeeeeeeee.....eeeeeee.hhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rzm A  -2 GRHMPAETVRKEVALEYCRRVNAGELEGVLQLFAPDARLVDPLGTEPVVGRAALAARLAPALRGAVHEEPGRPYAAHDGTSVVLPATVTVRGRTRVMGVIEVGEDGLIREMRVMWGVTDSSWTARPAPDEERRKELAREHCLRINDGDVDGLLKLYSPRIRFEDPVGSWTRTGLEALRAHATMAVGSNVRETAGLTVAGQDGRHAAVTVSATMDYLPSGPLLARHHLMTLPAPADPHRALIGIEYVMVIGVDADGLIDEMRAYWGATDVSLLDP 280
                                     7        17        27        37        47        57        67        77        87|      106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276    
                                                                                                                    87|                                                                                                                                                                                       
                                                                                                                     97                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.......eehhhhhhhhhhhhhhh..eeee..........eeeeeeeeee.....hhhhheeeeeeeeeee.....eeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeee.......eehhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeeeeehhhhhhhhhhh..............eeeeeeeeeeee.....eeeeeee.hhh.eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rzm B  -2 GRHMPAETVRKEVALEYCRRVNAGELEGVLQLFAPDARLVDPLGTEPVVGRAALAARLAPALRGAVHEEPGRPYAAHDGTSVVLPATVTVGAPGAPPQRRGRTRVMGVIEVGEDGLIREMRVMWGVTDSSWTARPAPDEERRKELAREHCLRINDGDVDGLLKLYSPRIRFEDPVGSWTRTGLEALRAHATMAVGSNVRETAGLTVAGQDGRHAAVTVSATMDYLPSGPLLARHHLMTLPAPADPHRALIGIEYVMVIGVDADGLIDEMRAYWGATDVSLLDP 280
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   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 4RZM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RZM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RZM)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        LSD19_STRLS | B6ZK72: 3rga

(-) Related Entries Specified in the PDB File

3rga EPOXIDE HYDROLASE COMPLEXED WITH A DIFFERENT LIGAND