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(-) Description

Title :  THE CRYSTAL STRUCTURE OF BIOTIN SYNTHASE, AN S-ADENOSYLMETHIONINE-DEPENDENT RADICAL ENZYME
 
Authors :  F. Berkovitch, Y. Nicolet, J. T. Wan, J. T. Jarrett, C. L. Drennan
Date :  30 Sep 03  (Deposition) - 13 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sam Radical Protein, Tim Barrel, Fes Cluster, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Berkovitch, Y. Nicolet, J. T. Wan, J. T. Jarrett, C. L. Drennan
Crystal Structure Of Biotin Synthase, An S-Adenosylmethionine-Dependent Radical Enzyme.
Science V. 303 76 2004
PubMed-ID: 14704425  |  Reference-DOI: 10.1126/SCIENCE.1088493
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIOTIN SYNTHASE
    Chains: A, B
    EC Number: 2.8.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21D(+)
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BIOB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: BIOTIN SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1DTB2Ligand/Ion6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3SAM2Ligand/IonS-ADENOSYLMETHIONINE
4SF42Ligand/IonIRON/SULFUR CLUSTER
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:59 , PRO A:61 , ALA A:100 , TRP A:102 , GLY A:132 , ASN A:153 , ASP A:155 , ARG A:173 , ILE A:192 , LEU A:224 , VAL A:225 , LEU A:291 , SF4 A:401 , DTB A:502BINDING SITE FOR RESIDUE SAM A 501
2AC2SOFTWARETYR B:59 , ALA B:100 , TRP B:102 , GLY B:132 , ASN B:153 , ASP B:155 , ARG B:173 , ILE B:192 , MET B:223 , LEU B:224 , VAL B:225 , LEU B:291 , SF4 B:401 , DTB B:502BINDING SITE FOR RESIDUE SAM B 501
3AC3SOFTWARECYS A:53 , GLU A:55 , CYS A:57 , CYS A:60 , SAM A:501BINDING SITE FOR RESIDUE SF4 A 401
4AC4SOFTWARECYS A:97 , CYS A:128 , CYS A:188 , ARG A:260BINDING SITE FOR RESIDUE FES A 402
5AC5SOFTWARECYS B:53 , CYS B:57 , CYS B:60 , SAM B:501BINDING SITE FOR RESIDUE SF4 B 401
6AC6SOFTWAREARG B:95 , CYS B:97 , CYS B:128 , CYS B:188 , ARG B:260BINDING SITE FOR RESIDUE FES B 402
7AC7SOFTWARELEU A:45 , ASN A:151 , ASN A:153 , ASN A:222 , ALA A:263 , PHE A:285 , LEU A:291 , THR A:292 , THR A:293 , SAM A:501BINDING SITE FOR RESIDUE DTB A 502
8AC8SOFTWAREASN B:151 , ASN B:153 , ASN B:222 , ALA B:263 , PHE B:285 , LEU B:290 , LEU B:291 , THR B:292 , THR B:293 , SAM B:501BINDING SITE FOR RESIDUE DTB B 502
9AC9SOFTWARELYS A:121 , ALA A:143 , GLU A:266 , GLU A:297BINDING SITE FOR RESIDUE TRS A 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R30)

(-) Exons   (0, 0)

(no "Exon" information available for 1R30)

(-) 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:312
 aligned with BIOB_ECOLI | P12996 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
           BIOB_ECOLI     4 RPRWTLSQVTELFEKPLLDLLFEAQQVHRQHFDPRQVQVSTLLSIKTGACPEDCKYCPQSSRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMPYLEQMVQGVKAMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPEFYGNIITTRTYQERLDTLEKVRDAGIKVCSGGIVGLGETVKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIRTIAVARIMMPTSYVRLSAGREQMNEQTQAMCFMAGANSIFYGCKLLTTPNPEEDKDLQLFRKLGLNPQQT 315
               SCOP domains d1r30a_ A: Biotin synthase                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1r30A00 A:4-315 Aldolase class I                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...........................hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee.....hhhhhhhhh...hhhhhhhhhhhhhhhhheee..eee....hhhhhhhhhhhhhh......eeeeee...............hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r30 A   4 RPRWTLSQVTELFEKPLLDLLFEAQQVHRQHFDPRQVQVSTLLSIKTGACPEDCKYCPQSSRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMPYLEQMVQGVKAMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPEFYGNIITTRTYQERLDTLEKVRDAGIKVCSGGIVGLGETVKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIRTIAVARIMMPTSYVRLSAGREQMNEQTQAMCFMAGANSIFYGCKLLTTPNPEEDKDLQLFRKLGLNPQQT 315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with BIOB_ECOLI | P12996 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:313
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312   
           BIOB_ECOLI     3 HRPRWTLSQVTELFEKPLLDLLFEAQQVHRQHFDPRQVQVSTLLSIKTGACPEDCKYCPQSSRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMPYLEQMVQGVKAMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPEFYGNIITTRTYQERLDTLEKVRDAGIKVCSGGIVGLGETVKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIRTIAVARIMMPTSYVRLSAGREQMNEQTQAMCFMAGANSIFYGCKLLTTPNPEEDKDLQLFRKLGLNPQQT 315
               SCOP domains d1r30b_ B: Biotin synthase                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1r30B00 B:3-315 Aldolase class I                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) --------------------------------------------Radical_SAM-1r30B03 B:47-209                                                                                                                                       ----------BATS-1r30B01 B:220-312                                                                       --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------Radical_SAM-1r30B04 B:47-209                                                                                                                                       ----------BATS-1r30B02 B:220-312                                                                       --- Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...........................hhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eee.....hhhhhhhhh...hhhhhhhhhhhhhhhhheee..eee....hhhhhhhhhhhhhh......eeeeee...............hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh..eee...........hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r30 B   3 HRPRWTLSQVTELFEKPLLDLLFEAQQVHRQHFDPRQVQVSTLLSIKTGACPEDCKYCPQSSRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKNPHERDMPYLEQMVQGVKAMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPEFYGNIITTRTYQERLDTLEKVRDAGIKVCSGGIVGLGETVKDRAGLLLQLANLPTPPESVPINMLVKVKGTPLADNDDVDAFDFIRTIAVARIMMPTSYVRLSAGREQMNEQTQAMCFMAGANSIFYGCKLLTTPNPEEDKDLQLFRKLGLNPQQT 315
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: BATS] (1)
(-)
Clan: no clan defined [family: Radical_SAM] (7)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BIOB_ECOLI | P12996)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0004076    biotin synthase activity    Catalysis of the reaction: 2 S-adenosyl-L-methionine + dethiobiotin + S(2-) = 2 5'-deoxyadenosine + 2 L-methionine + biotin + H(+).
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
biological process
    GO:0009102    biotin biosynthetic process    The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.

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  1r30
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