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(-) Description

Title :  LUMAZINE SYNTHASE FROM SACCHAROMYCES CEREVISIAE
 
Authors :  W. Meining, S. Mortl, M. Fischer, M. Cushman, A. Bacher, R. Ladenstein
Date :  02 Mar 00  (Deposition) - 02 Mar 01  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Lumazine Synthase, Saccharomyces Cerevisiae, X-Ray Structure Analysis, Inhibitor Complex, Vitamin Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Meining, S. Mortl, M. Fischer, M. Cushman, A. Bacher, R. Ladenstein
The Atomic Structure Of Pentameric Lumazine Synthase From Saccharomyces Cerevisiae At 1. 85 A Resolution Reveals The Binding Mode Of A Phosphonate Intermediate Analogue.
J. Mol. Biol. V. 299 181 2000
PubMed-ID: 10860731  |  Reference-DOI: 10.1006/JMBI.2000.3742
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LUMAZINE 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
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1INJ5Ligand/Ion5-(6-D-RIBITYLAMINO-2,4-DIHYDROXYPYRIMIDIN-5-YL)-1-PENTYL-PHOSPHONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:26 , ASN A:27 , GLY A:59 , SER A:60 , TYR A:61 , GLU A:62 , VAL A:89 , LEU A:90 , ILE A:91 , GLY A:93 , SER A:94 , THR A:95 , ILE A:101 , HOH A:205 , HOH A:221 , HOH A:295 , HOH A:296 , HOH A:297 , ILE B:121 , PHE B:122 , ARG B:136 , TRP B:152BINDING SITE FOR RESIDUE INJ A 200
2AC2SOFTWARETRP B:26 , ASN B:27 , GLY B:59 , SER B:60 , TYR B:61 , GLU B:62 , VAL B:89 , LEU B:90 , ILE B:91 , GLY B:93 , SER B:94 , THR B:95 , ILE B:101 , HOH B:320 , HOH B:336 , HOH B:398 , HOH B:401 , HOH B:407 , HOH B:408 , HOH B:409 , ILE C:121 , PHE C:122 , ARG C:136 , TRP C:152BINDING SITE FOR RESIDUE INJ B 300
3AC3SOFTWARETRP C:26 , GLY C:59 , SER C:60 , TYR C:61 , GLU C:62 , VAL C:89 , LEU C:90 , ILE C:91 , GLY C:93 , SER C:94 , THR C:95 , ILE C:101 , HOH C:409 , HOH C:434 , HOH C:483 , HOH C:1310 , HOH C:1356 , HOH C:1378 , ILE D:121 , PHE D:122 , ARG D:136 , TRP D:152BINDING SITE FOR RESIDUE INJ C 400
4AC4SOFTWARETRP D:26 , GLY D:59 , SER D:60 , TYR D:61 , GLU D:62 , VAL D:89 , LEU D:90 , ILE D:91 , GLY D:93 , SER D:94 , THR D:95 , ILE D:101 , HOH D:609 , HOH D:634 , HOH D:683 , HOH D:890 , HOH D:1510 , HOH D:1529 , HOH D:1556 , HOH D:1578 , ILE E:121 , PHE E:122 , ARG E:136BINDING SITE FOR RESIDUE INJ D 600
5AC5SOFTWAREILE A:121 , PHE A:122 , ARG A:136 , TRP A:152 , HOH A:300 , TRP E:26 , ASN E:27 , GLY E:59 , SER E:60 , TYR E:61 , GLU E:62 , VAL E:89 , LEU E:90 , ILE E:91 , GLY E:93 , SER E:94 , THR E:95 , HOH E:804 , HOH E:807 , HOH E:824 , HOH E:840 , HOH E:877 , HOH E:911 , HOH E:912 , HOH E:913BINDING SITE FOR RESIDUE INJ E 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 5)

Asymmetric/Biological Unit (1, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOL143C1YOL143C.1XV:55103-54594510RIB4_YEAST1-1691695A:1-168
B:1-168
C:1-168
D:1-168
E:1-168		168
168
168
168
168

(-) 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:168
 aligned with RIB4_YEAST | P50861 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           RIB4_YEAST     2 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 169
               SCOP domains d1ejba_ A: Lumazine synthase                                                                                                                                             SCOP domains
               CATH domains 1ejbA00 A:1-168  [code=3.40.50.960, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee...hhhhhhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-168 UniProt: 1-169 [INCOMPLETE]                                                                                                                       Transcript 1
                 1ejb A   1 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain B from PDB  Type:PROTEIN  Length:168
 aligned with RIB4_YEAST | P50861 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           RIB4_YEAST     2 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 169
               SCOP domains d1ejbb_ B: Lumazine synthase                                                                                                                                             SCOP domains
               CATH domains 1ejbB00 B:1-168  [code=3.40.50.960, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee...hhhhhhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-168 UniProt: 1-169 [INCOMPLETE]                                                                                                                       Transcript 1
                 1ejb B   1 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain C from PDB  Type:PROTEIN  Length:168
 aligned with RIB4_YEAST | P50861 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           RIB4_YEAST     2 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 169
               SCOP domains d1ejbc_ C: Lumazine synthase                                                                                                                                             SCOP domains
               CATH domains 1ejbC00 C:1-168  [code=3.40.50.960, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee...hhhhhhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-168 UniProt: 1-169 [INCOMPLETE]                                                                                                                       Transcript 1
                 1ejb C   1 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain D from PDB  Type:PROTEIN  Length:168
 aligned with RIB4_YEAST | P50861 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           RIB4_YEAST     2 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 169
               SCOP domains d1ejbd_ D: Lumazine synthase                                                                                                                                             SCOP domains
               CATH domains 1ejbD00 D:1-168  [code=3.40.50.960, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee...hhhhhhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-168 UniProt: 1-169 [INCOMPLETE]                                                                                                                       Transcript 1
                 1ejb D   1 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        


Chain E from PDB  Type:PROTEIN  Length:168
 aligned with RIB4_YEAST | P50861 from UniProtKB/Swiss-Prot  Length:169

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           RIB4_YEAST     2 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 169
               SCOP domains d1ejbe_ E: Lumazine synthase                                                                                                                                             SCOP domains
               CATH domains 1ejbE00 E:1-168  [code=3.40.50.960, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................eeeee...hhhhhhhhhhhhhhhhhhh..hhh.eeeee..hhhhhhhhhhhhhhhhhhh.....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhh.........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: E:1-168 UniProt: 1-169 [INCOMPLETE]                                                                                                                       Transcript 1
                 1ejb E   1 AVKGLGKPDQVYDGSKIRVGIIHARWNRVIIDALVKGAIERMASLGVEENNIIIETVPGSYELPWGTKRFVDRQAKLGKPLDVVIPIGVLIKGSTMHFEYISDSTTHALMNLQEKVDMPVIFGLLTCMTEEQALARAGIDEAHSMHNHGEDWGAAAVEMAVKFGKNAF 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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  (1, 5)

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

(-) CATH Domains  (1, 5)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (RIB4_YEAST | P50861)
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: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:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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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  1ejb
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  2.5.1.78
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1c2y CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY
1c41 CRYSTAL STRUCTURES OF A PENTAMERIC FUNGAL AND AN ICOSAHEDRAL PLANT LUMAZINE SYNTHASE REVEALS THE STRUCTURAL BASIS FOR DIFFERENCES IN ASSEMBLY
1di0 CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM BRUCELLA ABORTUS
1rvv SYNTHASE/RIBOFLAVIN SYNTHASE COMPLEX OF BACILLUS SUBTILIS