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(-) Description

Title :  CRYSTAL STRUCTURE AND MECHANISM OF A BACTERIAL FLUORINATING ENZYME
 
Authors :  C. Dong, F. Huang, H. Deng, C. Schaffrath, J. B. Spencer, D. O'Hagan, J. H
Date :  06 Dec 03  (Deposition) - 02 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Fluorinase, Central 7 Stranded Beta Sheets, Anti-Parallel Beta Sheets, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dong, F. Huang, H. Deng, C. Schaffrath, J. B. Spencer, D. O'Hagan, J. H. Naismith
Crystal Structure And Mechanism Of A Bacterial Fluorinating Enzyme
Nature V. 427 561 2004
PubMed-ID: 14765200  |  Reference-DOI: 10.1038/NATURE02280
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
    Chains: A, B, C
    EC Number: 2.5.1.63
    Organism Scientific: STREPTOMYCES CATTLEYA
    Organism Taxid: 29303
    Strain: NRRL8057

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SAM3Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SAM6Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SAM6Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , ASP A:21 , SER A:23 , TRP A:50 , TYR A:77 , PRO A:78 , THR A:80 , THR A:155 , PHE A:156 , SER A:158 , HOH A:505 , HOH A:511 , ASP B:210 , PHE B:213 , ASN B:215 , TRP B:217 , PHE B:254 , SER B:269 , ARG B:270 , ARG B:277 , ALA B:279BINDING SITE FOR RESIDUE SAM A 500
2AC2SOFTWAREASP B:16 , LEU B:17 , ASP B:21 , SER B:23 , TRP B:50 , TYR B:77 , PRO B:78 , THR B:155 , PHE B:156 , SER B:158 , HOH B:516 , HOH B:596 , ASP C:210 , PHE C:213 , ASN C:215 , TRP C:217 , PHE C:254 , SER C:269 , ARG C:270 , ARG C:277 , ALA C:279BINDING SITE FOR RESIDUE SAM B 500
3AC3SOFTWAREASP A:210 , PHE A:213 , ASN A:215 , TRP A:217 , PHE A:254 , SER A:269 , ARG A:270 , ARG A:277 , ALA A:279 , ASP C:16 , ASP C:21 , SER C:23 , TRP C:50 , TYR C:77 , PRO C:78 , THR C:155 , PHE C:156 , SER C:158 , HOH C:512 , HOH C:514BINDING SITE FOR RESIDUE SAM C 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RQP)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1His A:211 -Pro A:212
2His B:211 -Pro B:212
3His C:211 -Pro C:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RQP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RQP)

(-) Exons   (0, 0)

(no "Exon" information available for 1RQP)

(-) 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 d1rqpa2 A:8-192 5'-fluoro-5'-deoxyadenosine synthase                                                                                                                                     d1rqpa1 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..........................eeee.....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhhh.......eeeeee...eeeeeeee.hhhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqp 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 d1rqpb2 B:8-192 5'-fluoro-5'-deoxyadenosine synthase                                                                                                                                     d1rqpb1 B:193-298 5'-fluoro-5'-deoxyadenosine synthase                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh...eeee........hhhhhhhhhh.hhhhh....eeeee..........eeeeee..........................eeeee....hhhhhhhhheeeeee..............hhhhhhhhhhhhhhhh..hhhhh....hhhhh........eee..eeeeeeeeee....eeeeeeehhhhh........eeeeee...eeeeee...hhhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqp 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 d1rqpc2 C:8-192 5'-fluoro-5'-deoxyadenosine synthase                                                                                                                                     d1rqpc1 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.hhhhhh....eeeee....eeeeee....hhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rqp 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 1RQP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RQP)

(-) 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: 1rqr 2c2w 2c4t 2c4u 2c5b 2c5h 2cbx 2cc2 2v7t 2v7u 2v7v 2v7w 2v7x 4cqj 5fiu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RQP)