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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF 5'-FLUORODEOXYADENOSINE SYNTHASE FROM STREPTOMYCES CATTLEYA COMPLEXED WITH 5'-FLUORODEOXYADENOSINE
 
Authors :  X. Zhu, D. O'Hagan, J. H. Naismith
Date :  02 Aug 07  (Deposition) - 12 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Transferase, Mechanism Of Fluorination, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zhu, D. A. Robinson, A. R. Mcewan, D. O'Hagan, J. H. Naismith
Mechanism Of Enzymatic Fluorination In Streptomyces Cattleya.
J. Am. Chem. Soc. V. 129 14597 2007
PubMed-ID: 17985882  |  Reference-DOI: 10.1021/JA0731569

(-) Compounds

Molecule 1 - 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
    Atcc: 9747
    Chains: A, B, C
    EC Number: 2.5.1.63
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEHISTEV-FLA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: C43
    Expression System Vector: PEHISTEV
    Organism Scientific: STREPTOMYCES CATTLEYA
    Organism Taxid: 29303

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
15FD3Ligand/Ion5'-FLUORO-5'-DEOXYADENOSINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
15FD6Ligand/Ion5'-FLUORO-5'-DEOXYADENOSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , TRP A:50 , THR A:76 , TYR A:77 , PRO A:78 , THR A:80 , THR A:155 , PHE A:156 , TYR A:157 , SER A:158 , PHE B:213 , ASN B:215 , PHE B:254 , ARG B:277 , ALA B:279BINDING SITE FOR RESIDUE 5FD A1299
2AC2SOFTWAREASP B:16 , TRP B:50 , TYR B:77 , PRO B:78 , THR B:80 , THR B:155 , PHE B:156 , TYR B:157 , SER B:158 , PHE C:213 , ASN C:215 , PHE C:254 , ARG C:277 , ALA C:279BINDING SITE FOR RESIDUE 5FD C1299
3AC3SOFTWAREPHE A:213 , ASN A:215 , PHE A:254 , ARG A:277 , ALA A:279 , ASP C:16 , TRP C:50 , THR C:76 , TYR C:77 , PRO C:78 , THR C:80 , THR C:155 , PHE C:156 , TYR C:157 , SER C:158BINDING SITE FOR RESIDUE 5FD C1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V7V)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Asp A:198 -Gly A:199
2His A:211 -Pro A:212
3Gly B:199 -Glu B:200
4His B:211 -Pro B:212
5His C:211 -Pro C:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V7V)

(-) Exons   (0, 0)

(no "Exon" information available for 2V7V)

(-) 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:291
 aligned with FLA_STRCT | Q70GK9 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:291
                                    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       287       297 
            FLA_STRCT     8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
               SCOP domains d2v7va2 A:8-192 5'-fluoro-5'-deoxyadenosine synthase                                                                                                                                     d2v7va1 A:193-298 5'-fluoro-5'-deoxyadenosine synthase                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeeeee......hhhhhhhh...hhhhh....eeeee...........eeeee...hhhhh..................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........ee....eeeeeeeee....eeeeeeehhhhhhh......eeeeee...eeeeeeee.hhhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v7v A   8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
                                    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       287       297 


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with FLA_STRCT | Q70GK9 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:291
                                    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       287       297 
            FLA_STRCT     8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
               SCOP domains d2v7vb2 B:8-192 5'-fluoro-5'-deoxyadenosine synthase                                                                                                                                     d2v7vb1 B:193-298 5'-fluoro-5'-deoxyadenosine synthase                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeeeee......hhhhhhhh...hhhhh....eeeee...........eeeee..........................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhhh.......eeeeee...eeeeeeee.hhhhhh....eeeee....eeeeee...............eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v7v B   8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
                                    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       287       297 


Chain C from PDB  Type:PROTEIN  Length:291
 aligned with FLA_STRCT | Q70GK9 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:291
                                    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       287       297 
            FLA_STRCT     8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
               SCOP domains d2v7vc2 C:8-192 5'-fluoro-5'-deoxyadenosine synthase                                                                                                                                     d2v7vc1 C:193-298 5'-fluoro-5'-deoxyadenosine synthase                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeee........hhhhhhhh...hhhhh....eeeee...........eeeee..........................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhh........eeeeee...eeeeeeee..hhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v7v C   8 RPIIAFMSDLGTTDDSVAQCKGLMYSICPDVTVVDVCHSMTPWDVEEGARYIVDLPRFFPEGTVFATTTYPATGTTTRSVAVRIKQAAKGGARGQWAGSGAGFERAEGSYIYIAPNNGLLTTVLEEHGYLEAYEVTSPKVIPEQPEPTFYSREMVAIPSAHLAAGFPLSEVGRPLEDHEIVRFNRPAVEQDGEALVGVVSAIDHPFGNVWTNIHRTDLEKAGIGYGARLRLTLDGVLPFEAPLTPTFADAGEIGNIAIYLNSRGYLSIARNAASLAYPYHLKEGMSARVEA 298
                                    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       287       297
   Legend:   → Mismatch (orange background)
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  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  (2, 6)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V7V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V7V)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (FLA_STRCT | Q70GK9)
molecular function
    GO:0033846    adenosyl-fluoride synthase activity    Catalysis of the reaction: S-adenosyl-L-methionine + fluoride = 5'-deoxy-5'-fluoroadenosine + L-methionine.
    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.

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  2.5.1.63
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 Related Entries

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

UniProtKB/Swiss-Prot
        FLA_STRCT | Q70GK9: 1rqp 1rqr 2c2w 2c4t 2c4u 2c5b 2c5h 2cbx 2cc2 2v7t 2v7u 2v7w 2v7x 4cqj 5fiu

(-) Related Entries Specified in the PDB File

1rqp CRYSTAL STRUCTURE AND MECHANISM OF A BACTERIAL FLUORINATINGENZYME
1rqr CRYSTAL STRUCTURE AND MECHANISM OF A BACTERIAL FLUORINATINGENZYME, PRODUCT COMPLEX
2c2w THE FLUORINASE FROM STREPTOMYCES CATTLEYA IS ALSO A CHLORINASE. STRUCTURE OF 5'-CHLORO- 5'-DEOXYADENOSINE CRSTALLISED IN THE FLUORINASE.
2c4t X-RAY CRYSTAL STRUCTURE OF 5'- FLUORODEOXYADENOSINE SYNTHASE FROM STREPTOMYCES CATTLEYA COMPLEXED WITH AN INHIBITOR, AN ANALOGUE OF S-ADENOSYL METHIONINE
2c4u CRYSTAL STRUCTURE OF THE APO FORM OF THE 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE ENZYME FROM STREPTOMYCES CATTLEYA
2c5b X-RAY CRYSTAL STRUCTUE OF 5'- FLUORODEOXYADENOSINE SYNTHASE FROM STREPTOMYCES CATTLEYA COMPLEXED WITH 2'DEOXY-5'DEOXY- FLUOROADENOSINE.
2c5h X-RAY CRYSTAL STRUCTURE OF 5- FLUORODEOXYADENOSINE SYNTHASE FROM STREPTOMYCES CATTLEYA COMPLEXED WITH 5-DEOXY-ADENOSINE
2cbx X-RAY CRYSTAL STRUCTURE OF 5'- FLUORODEOXYADENOSINE SYNTHASE FROM STREPTOMYCES CATTLEYA COMPLEXED WITH BETA-D- ERYTHROFURANOSYL-ADENOSINE
2cc2 X-RAY CRYSTAL STRUCTURE OF 5'- FLUORODEOXYADENOSINE SYNTHASE FROM STREPTOMYCES CATTLEYA COMPLEXED WITH 5'DEOXYADENOSINE
2v7t THE STRUCTURAL BASIS OF THE MECHANISM OF THE FLUORINASE IN STREPTOMYCES CATTLEYA
2v7u THE STRUCTURAL BASIS OF THE MECHANISM OF THE FLUORINASE IN STREPTOMYCES CATTLEYA
2v7w X-RAY CRYSTAL STRUCTURE OF 5'- FLUORODEOXYADENOSINE SYNTHASE S158G MUTANT FROM STREPTOMYCES CATTLEYA COMPLEXED WITH 5'DEOXY - FLUOROADENOSINE
2v7x X-RAY CRYSTAL STRUCTURE OF 5'- FLUORODEOXYADENOSINE SYNTHASE S158A MUTANT FROM STREPTOMYCES CATTLEYA COMPLEXED WITH THE PRODUCTS, FDA AND MET