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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE
 
Authors :  D. -I. Liao, Z. Wawrzak, J. C. Calabrese, P. V. Viitanen, D. B. Jordan
Date :  13 Mar 01  (Deposition) - 19 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Riboflavin Synthase, Riboflavin Biosynthesis, Antimicrobial Target, Structure-Based Design, Escherichia Coli, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. I. Liao, Z. Wawrzak, J. C. Calabrese, P. V. Viitanen, D. B. Jordan
Crystal Structure Of Riboflavin Synthase.
Structure V. 9 399 2001
PubMed-ID: 11377200  |  Reference-DOI: 10.1016/S0969-2126(01)00600-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOFLAVIN SYNTHASE
    ChainsA, B, C
    EC Number2.5.1.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-24A(+) (NOVAGEN)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneBACTERIA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1I8D)

(-) Sites  (0, 0)

(no "Site" information available for 1I8D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I8D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I8D)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LUMAZINE_BINDPS51177 Riboflavin synthase alpha chain lumazine-binding repeat profile.RISA_ECOLI1-97
 
 
98-195
 
 
  6A:1-97
B:1-97
C:1-97
A:98-195
B:98-195
C:98-195
RISA_SHIFL1-97
 
 
98-195
 
 
  6A:1-97
B:1-97
C:1-97
A:98-195
B:98-195
C:98-195

(-) Exons   (0, 0)

(no "Exon" information available for 1I8D)

(-) 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:206
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           RISA_ECOLI     1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
               SCOP domains d1i8da1 A:1-93 Riboflavin synthase                                                           d1i8da2 A:94-206 Riboflavin synthase                                                                              SCOP domains
               CATH domains 1i8dA01 A:1-89  [code=2.40.30.20, no name defined]                                       ------------1i8dA02 A:102-206  [code=2.40.30.20, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeeee..................eeeeeeeeeee..eeeeeeee.hhhhhhhh....eeee..eeee.......eeeeeehhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: A:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: A:98-195 UniProt: 98-195                                                      ----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8d A   1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      

Chain A from PDB  Type:PROTEIN  Length:206
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           RISA_SHIFL     1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
               SCOP domains d1i8da1 A:1-93 Riboflavin synthase                                                           d1i8da2 A:94-206 Riboflavin synthase                                                                              SCOP domains
               CATH domains 1i8dA01 A:1-89  [code=2.40.30.20, no name defined]                                       ------------1i8dA02 A:102-206  [code=2.40.30.20, no name defined]                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeeee..................eeeeeeeeeee..eeeeeeee.hhhhhhhh....eeee..eeee.......eeeeeehhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: A:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: A:98-195 UniProt: 98-195                                                      ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8d A   1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           RISA_ECOLI     1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
               SCOP domains d1i8db1 B:1-93 Riboflavin synthase                                                           d1i8db2 B:94-206 Rib     oflavin synthase                                                                         SCOP domains
               CATH domains 1i8dB01 B:1-89  [code=2.40.30.20, no name defined]                                       ------------1i8dB02 B:10     2-205  [code=2.40.30.20, no name defined]                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeeee..................eeeeeeee.-----.eeeeee.hhhhhhhh....eeee..eeeeeeee...eeeee.hhhhhh..hhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: B:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: B:98-195 UniProt: 98-195                                                      ----------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8d B   1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKIL-----RQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
                                    10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150       160       170       180       190       200      
                                                                                                                                          113   119                                                                                       

Chain B from PDB  Type:PROTEIN  Length:201
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           RISA_SHIFL     1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
               SCOP domains d1i8db1 B:1-93 Riboflavin synthase                                                           d1i8db2 B:94-206 Rib     oflavin synthase                                                                         SCOP domains
               CATH domains 1i8dB01 B:1-89  [code=2.40.30.20, no name defined]                                       ------------1i8dB02 B:10     2-205  [code=2.40.30.20, no name defined]                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeeee..................eeeeeeee.-----.eeeeee.hhhhhhhh....eeee..eeeeeeee...eeeee.hhhhhh..hhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: B:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: B:98-195 UniProt: 98-195                                                      ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8d B   1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKIL-----RQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAARENAM 206
                                    10        20        30        40        50        60        70        80        90       100       110  |    120       130       140       150       160       170       180       190       200      
                                                                                                                                          113   119                                                                                       

Chain C from PDB  Type:PROTEIN  Length:185
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           RISA_ECOLI     1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAA 201
               SCOP domains d1i8dc1 C:1-90 Riboflavin synthase                                                              d1i8dc2 C:97-2          01 Riboflavin synthase                                                            SCOP domains
               CATH domains 1i8dC01 C:1-89  [code=2.40.30.20, no name defined]                                       -      -----1i8dC02 C          :102-199  [code=2.40.30.20, no name defined]                                   -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeee....------........eeeee.----------.eeee.hhhhhhhh....eeee..eeeeeeee...eeee..hhhhhhhh.........eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: C:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: C:98-195 UniProt: 98-195                                                      ------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8d C   1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKF------HLMSGHIMTTAEVA----------IWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAA 201
                                    10        20        30        40        50        60        70        80        90      |100       110         -|      130       140       150       160       170       180       190       200 
                                                                                                                    90     97          110        121                                                                                

Chain C from PDB  Type:PROTEIN  Length:185
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           RISA_SHIFL     1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKFSDEIGGHLMSGHIMTTAEVAKILTSENNRQIWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAA 201
               SCOP domains d1i8dc1 C:1-90 Riboflavin synthase                                                              d1i8dc2 C:97-2          01 Riboflavin synthase                                                            SCOP domains
               CATH domains 1i8dC01 C:1-89  [code=2.40.30.20, no name defined]                                       -      -----1i8dC02 C          :102-199  [code=2.40.30.20, no name defined]                                   -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeee....------........eeeee.----------.eeee.hhhhhhhh....eeee..eeeeeeee...eeee..hhhhhhhh.........eeeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: C:1-97 UniProt: 1-97                                                         LUMAZINE_BIND  PDB: C:98-195 UniProt: 98-195                                                      ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i8d C   1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERAAKF------HLMSGHIMTTAEVA----------IWFKVQDSQLMKYILYKGFIGIDGISLTVGEVTPTRFCVHLIPETLERTTLGKKKLGARVNIEIDPQTQAVVDTVERVLAA 201
                                    10        20        30        40        50        60        70        80        90      |100       110         -|      130       140       150       160       170       180       190       200 
                                                                                                                    90     97          110        121                                                                                

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I8D)

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (RISA_SHIFL | P0AFU9)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004746    riboflavin synthase activity    Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + riboflavin.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

Chain A,B,C   (RISA_ECOLI | P0AFU8)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004746    riboflavin synthase activity    Catalysis of the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine + H(+) = 5-amino-6-(D-ribitylamino)uracil + riboflavin.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RISA_ECOLI | P0AFU81hze 1i18 1pkv
        RISA_SHIFL | P0AFU91hze 1i18 1pkv

(-) Related Entries Specified in the PDB File

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