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(-) Description

Title :  THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE IN COMPLEX WITH RIBOFLAVIN
 
Authors :  W. Meining, S. Eberhardt, A. Bacher, R. Ladenstein
Date :  06 Jun 03  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Beta-Barrel, Greek Key Motif, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Meining, S. Eberhardt, A. Bacher, R. Ladenstein
The Structure Of The N-Terminal Domain Of Riboflavin Synthase In Complex With Riboflavin At 2. 6A Resolution.
J. Mol. Biol. V. 331 1053 2003
PubMed-ID: 12927541  |  Reference-DOI: 10.1016/S0022-2836(03)00844-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOFLAVIN SYNTHASE ALPHA CHAIN
    Chains: A, B
    EC Number: 2.5.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: XL1-BLUE CELLS
    Expression System Taxid: 562
    Expression System Vector: PNCO113
    Fragment: N-TERMINAL DOMAIN
    Gene: RIBE OR RIBC OR B1662 OR SF1690
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1RBF2Ligand/IonRIBOFLAVIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:47 , CYS A:48 , LEU A:49 , THR A:50 , ASP A:62 , LEU A:63 , MET A:64 , THR A:67 , HOH A:101 , HOH A:114 , GLY B:4 , ILE B:5 , VAL B:6 , MET B:64 , GLU B:66 , RBF B:101BINDING SITE FOR RESIDUE RBF A 100
2AC2SOFTWAREGLY A:4 , ILE A:5 , VAL A:6 , THR A:50 , ASP A:62 , MET A:64 , RBF A:100 , CYS B:47 , CYS B:48 , LEU B:49 , THR B:50 , ASP B:62 , LEU B:63 , MET B:64 , THR B:67 , THR B:71 , HOH B:102 , HOH B:103BINDING SITE FOR RESIDUE RBF B 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LUMAZINE_BINDPS51177 Riboflavin synthase alpha chain lumazine-binding repeat profile.RISA_ECOLI1-97
 
98-195		  2A:1-87
B:1-87
-
RISA_SHIFL1-97
 
98-195		  2A:1-87
B:1-87
-

(-) Exons   (0, 0)

(no "Exon" information available for 1PKV)

(-) 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:87
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
            RISA_ECOLI    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
               SCOP domains d1pkva_ A: Riboflavin synthase                                                          SCOP domains
               CATH domains 1pkvA00 A:1-87  [code=2.40.30.20, no name defined]                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: A:1-87 UniProt: 1-97                                                PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1pkv A  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
                                    10        20        30        40        50        60        70        80       


Chain A from PDB  Type:PROTEIN  Length:87
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
            RISA_SHIFL    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
               SCOP domains d1pkva_ A: Riboflavin synthase                                                          SCOP domains
               CATH domains 1pkvA00 A:1-87  [code=2.40.30.20, no name defined]                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeeehhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: A:1-87 UniProt: 1-97                                                PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1pkv A  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with RISA_ECOLI | P0AFU8 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
            RISA_ECOLI    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
               SCOP domains d1pkvb_ B: Riboflavin synthase                                                          SCOP domains
               CATH domains 1pkvB00 B:1-87  [code=2.40.30.20, no name defined]                                      CATH domains
           Pfam domains (1) --Lum_binding-1pkvB01 B:3-87                                                            Pfam domains (1)
           Pfam domains (2) --Lum_binding-1pkvB02 B:3-87                                                            Pfam domains (2)
         Sec.struct. author .......eeeeeeeeee....eeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: B:1-87 UniProt: 1-97                                                PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1pkv B  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
                                    10        20        30        40        50        60        70        80       


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with RISA_SHIFL | P0AFU9 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:87
                                    10        20        30        40        50        60        70        80       
            RISA_SHIFL    1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
               SCOP domains d1pkvb_ B: Riboflavin synthase                                                          SCOP domains
               CATH domains 1pkvB00 B:1-87  [code=2.40.30.20, no name defined]                                      CATH domains
           Pfam domains (1) --Lum_binding-1pkvB01 B:3-87                                                            Pfam domains (1)
           Pfam domains (2) --Lum_binding-1pkvB02 B:3-87                                                            Pfam domains (2)
         Sec.struct. author .......eeeeeeeeee....eeeeee.hhhhh.......eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) LUMAZINE_BIND  PDB: B:1-87 UniProt: 1-97                                                PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------- Transcript
                  1pkv B  1 MFTGIVQGTAKLVSIDEKPNFRTHVVELPDHMLDGLETGASVAHNGCCLTVTEINGNHVSFDLMKETLRITNLGDLKVGDWVNVERA 87
                                    10        20        30        40        50        60        70        80
   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: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: FAD_Lum_binding (30)

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

Chain A,B   (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).

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 Related Entries

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

UniProtKB/Swiss-Prot
        RISA_ECOLI | P0AFU8: 1hze 1i18 1i8d
        RISA_SHIFL | P0AFU9: 1hze 1i18 1i8d

(-) Related Entries Specified in the PDB File

1hze SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE FROM E. COLI
1i8d CRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE
1kzl RIBOFLAVIN SYNTHASE FROM S. POMBE BOUND TO CARBOXYETHYLLUMAZINE