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(-) Description

Title :  MUTANT ENZYME L119F LUMAZINE SYNTHASE FROM S.POMBE
 
Authors :  S. Gerhardt, I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bach R. Huber, M. Fischer
Date :  06 Feb 02  (Deposition) - 24 Jul 02  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  A,B,C,D,E  (2x)
Keywords :  Riboflavin Biosynthesis, Lumazine Synthase, Schizosaccharomyces Pombe, Ligand Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gerhardt, I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bacher, R. Huber, M. Fischer
The Structural Basis Of Riboflavin Binding To Schizosaccharomyces Pombe 6, 7-Dimethyl-8-Ribityllumazine Synthase.
J. Mol. Biol. V. 318 1317 2002
PubMed-ID: 12083520  |  Reference-DOI: 10.1016/S0022-2836(02)00116-X

(-) Compounds

Molecule 1 - 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
    Chains: A, B, C, D, E
    EC Number: 2.5.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO113
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABCDE
Biological Unit 2 (2x): ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1PO410Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:133 , GLY B:90 , SER B:91 , THR B:92 , HIS B:94BINDING SITE FOR RESIDUE PO4 B 1001
2AC2SOFTWAREARG D:133 , GLY E:90 , SER E:91 , THR E:92 , HIS E:94BINDING SITE FOR RESIDUE PO4 E 1002
3AC3SOFTWAREARG B:133 , GLY C:90 , SER C:91 , THR C:92BINDING SITE FOR RESIDUE PO4 C 1003
4AC4SOFTWAREGLY A:90 , SER A:91 , THR A:92 , HIS A:94 , HOH A:1005 , ARG E:133BINDING SITE FOR RESIDUE PO4 A 1004
5AC5SOFTWAREARG C:133 , GLY D:90 , SER D:91 , THR D:92 , HIS D:94BINDING SITE FOR RESIDUE PO4 D 1005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KZ9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 1KZ9)

(-) 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:147
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:147
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           RIB4_SCHPO    12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kz9a_ A: Lumazine synthase                                                                                                                        SCOP domains
               CATH domains 1kz9A00 A:12-158  [code=3.40.50.960, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kz9 A  12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:147
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           RIB4_SCHPO    12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kz9b_ B: Lumazine synthase                                                                                                                        SCOP domains
               CATH domains 1kz9B00 B:12-158  [code=3.40.50.960, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kz9 B  12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain C from PDB  Type:PROTEIN  Length:149
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:149
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           RIB4_SCHPO    11 SDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKALY 159
               SCOP domains d1kz9c_ C: Lumazine synthase                                                                                                                          SCOP domains
               CATH domains 1kz9C00 C:11-159  [code=3.40.50.960, no name defined]                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kz9 C  11 SDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKALY 159
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain D from PDB  Type:PROTEIN  Length:147
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:147
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       
           RIB4_SCHPO    12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kz9d_ D: Lumazine synthase                                                                                                                        SCOP domains
               CATH domains 1kz9D00 D:12-158  [code=3.40.50.960, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kz9 D  12 DLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain E from PDB  Type:PROTEIN  Length:152
 aligned with RIB4_SCHPO | Q9UUB1 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:152
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156  
           RIB4_SCHPO     7 GPNPSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVILGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
               SCOP domains d1kz9e_ E: Lumazine synthase                                                                                                                             SCOP domains
               CATH domains 1kz9E00 E:7-158  [code=3.40.50.960, no name defined]                                                                                                     CATH domains
           Pfam domains (1) --------DMRL_synthase-1kz9E01 E:15-157                                                                                                                 - Pfam domains (1)
           Pfam domains (2) --------DMRL_synthase-1kz9E02 E:15-157                                                                                                                 - Pfam domains (2)
           Pfam domains (3) --------DMRL_synthase-1kz9E03 E:15-157                                                                                                                 - Pfam domains (3)
           Pfam domains (4) --------DMRL_synthase-1kz9E04 E:15-157                                                                                                                 - Pfam domains (4)
           Pfam domains (5) --------DMRL_synthase-1kz9E05 E:15-157                                                                                                                 - Pfam domains (5)
         Sec.struct. author .............eeeeee..hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kz9 E   7 GPNPSDLKGPELRILIVHARWNLQAIEPLVKGAVETMIEKHDVKLENIDIESVPGSWELPQGIRASIARNTYDAVIGIGVLIKGSTMHFEYISEAVVHGLMRVGLDSGVPVIFGLLTVLNEEQALYRAGLNGGHNHGNDWGSAAVEMGLKAL 158
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156
   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, 5)

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

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: no clan defined [family: DMRL_synthase] (19)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RIB4_SCHPO | Q9UUB1)
molecular function
    GO:0000906    6,7-dimethyl-8-ribityllumazine synthase activity    Catalysis of the reaction: 3,4-dihydroxy-2-butanone-4-phosphate + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione = 6,7-dimethyl-8-ribityllumazine + phosphate.
    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:1902444    riboflavin binding    Interacting selectively and non-covalently with 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: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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0009349    riboflavin synthase complex    An flavoprotein that catalyzes the reaction the breakdown of dimethyl(ribityl)lumazine to form riboflavin and ribitylamino-amino-dihydroxypyrimidine.

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  1kz9
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  RIB4_SCHPO | Q9UUB1
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  2.5.1.78
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIB4_SCHPO | Q9UUB1: 1kyv 1kyx 1kyy 1kz1 1kz4 1kz6 2a57 2a58 2a59

(-) Related Entries Specified in the PDB File

1kyv 1KYV CONTAINS THE SAME PROTEIN COMPLEXED WITH RIBOFLAVIN.
1kyx 1KYX CONTAINS THE SAME PROTEIN COMPLEXED WITH CARBOXYETHYLLUMAZINE.
1kyy 1KYY CONTAINS THE SAME PROTEIN COMPLEXED WITH NITROPYRIMIDINEDIONE.
1kz1 1KZ1 CONTAINS THE SAME PROTEIN, W27G MUTANT.
1kz4 1KZ4 CONTAINS THE SAME PROTEIN, W63Y MUTANT.
1kz6 1KZ6 CONTAINS THE SAME PROTEIN, W63Y/L119F MUTANT.