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(-) Description

Title :  LUMAZINE SYNTHASE RIBH1 FROM BRUCELLA MELITENSIS (GENE BMEI1187, SWISS-PROT ENTRY Q8YGH2) COMPLEXED WITH INHIBITOR 5-NITRO-6-(D-RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE
 
Authors :  S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Br A. Bacher, M. Fischer, F. A. Goldbaum
Date :  07 Dec 06  (Deposition) - 14 Aug 07  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
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 :  Lumazine Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Braden, A. Bacher, M. Fischer, F. A. Goldbaum
Structural And Kinetic Properties Of Lumazine Synthase Isoenzymes In The Order Rhizobiales
J. Mol. Biol. V. 373 664 2007
PubMed-ID: 17854827  |  Reference-DOI: 10.1016/J.JMB.2007.08.021

(-) Compounds

Molecule 1 - 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE 1
    Chains: A, B, C, D, E
    EC Number: 2.5.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIBH1
    Organism Scientific: BRUCELLA MELITENSIS
    Organism Taxid: 29459
    Synonym: DMRL SYNTHASE 1, LUMAZINE SYNTHASE 1, RIBOFLAVIN SYNTHASE 1 BETA CHAIN

 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  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2INI5Mod. Residue5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2INI5Mod. Residue5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2INI10Mod. Residue5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:67 , GLU A:73 , ALA E:67 , GLU E:73BINDING SITE FOR RESIDUE CA A 301
02AC2SOFTWAREGLU A:124BINDING SITE FOR RESIDUE CA A 302
03AC3SOFTWAREALA B:67 , GLU B:73 , ALA D:67 , GLU D:73BINDING SITE FOR RESIDUE CA B 303
04AC4SOFTWAREALA C:67 , GLU C:73BINDING SITE FOR RESIDUE CA C 304
05AC5SOFTWAREHOH A:404 , GLU C:124BINDING SITE FOR RESIDUE CA C 305
06AC6SOFTWAREASP D:24 , ASP D:25 , ASP D:28 , HOH D:484BINDING SITE FOR RESIDUE CA D 306
07AC7SOFTWAREPHE A:22 , TYR A:23 , GLY A:52 , ALA A:53 , LEU A:54 , GLU A:55 , THR A:82 , VAL A:83 , HIS A:90 , VAL A:94 , HOH A:403 , ASN E:115 , PHE E:140BINDING SITE FOR RESIDUE INI A 201
08AC8SOFTWAREASN A:115 , PHE A:140 , PHE B:22 , TYR B:23 , GLY B:52 , ALA B:53 , LEU B:54 , GLU B:55 , THR B:82 , VAL B:83 , ILE B:84 , HIS B:90 , VAL B:94 , HOH B:422BINDING SITE FOR RESIDUE INI B 202
09AC9SOFTWAREGLY B:114 , ASN B:115 , PHE B:140 , ALA B:144 , PHE C:22 , TYR C:23 , GLY C:52 , ALA C:53 , LEU C:54 , GLU C:55 , THR C:82 , VAL C:83 , ILE C:84 , HIS C:90 , VAL C:94 , HOH C:438BINDING SITE FOR RESIDUE INI C 203
10BC1SOFTWAREASN C:115 , PHE C:140 , PHE D:22 , TYR D:23 , GLY D:52 , ALA D:53 , LEU D:54 , GLU D:55 , THR D:82 , VAL D:83 , ILE D:84 , HIS D:90 , VAL D:94BINDING SITE FOR RESIDUE INI D 204
11BC2SOFTWAREASN D:115 , PHE D:140 , PHE E:22 , TYR E:23 , GLY E:52 , ALA E:53 , LEU E:54 , GLU E:55 , THR E:82 , VAL E:83 , ILE E:84 , HIS E:90 , VAL E:94BINDING SITE FOR RESIDUE INI E 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O6H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O6H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O6H)

(-) Exons   (0, 0)

(no "Exon" information available for 2O6H)

(-) 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 RISB1_BRUME | Q8YGH2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:147
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       
          RISB1_BRUME    11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o6hA00 A:11-157  [code=3.40.50.960, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhhh.......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6h A  11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with RISB1_BRUME | Q8YGH2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:147
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       
          RISB1_BRUME    11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o6hB00 B:11-157  [code=3.40.50.960, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh.......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6h B  11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain C from PDB  Type:PROTEIN  Length:146
 aligned with RISB1_BRUME | Q8YGH2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:146
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151      
          RISB1_BRUME    12 APHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o6hC00 C:12-157  [code=3.40.50.960, no name defined]                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhh......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6h C  12 APHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151      


Chain D from PDB  Type:PROTEIN  Length:147
 aligned with RISB1_BRUME | Q8YGH2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:147
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       
          RISB1_BRUME    11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o6hD00 D:11-157  [code=3.40.50.960, no name defined]                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh.......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6h D  11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       


Chain E from PDB  Type:PROTEIN  Length:147
 aligned with RISB1_BRUME | Q8YGH2 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:147
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       
          RISB1_BRUME    11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2o6hE00 E:11-157  [code=3.40.50.960, no name defined]                                                                                               CATH domains
           Pfam domains (1) DMRL_synthase-2o6hE01 E:11-155                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) DMRL_synthase-2o6hE02 E:11-155                                                                                                                   -- Pfam domains (2)
           Pfam domains (3) DMRL_synthase-2o6hE03 E:11-155                                                                                                                   -- Pfam domains (3)
           Pfam domains (4) DMRL_synthase-2o6hE04 E:11-155                                                                                                                   -- Pfam domains (4)
           Pfam domains (5) DMRL_synthase-2o6hE05 E:11-155                                                                                                                   -- Pfam domains (5)
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh.......eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o6h E  11 DAPHLLIVEARFYDDLADALLDGAKAALDEAGATYDVVTVPGALEIPATISFALDGADNGGTEYDGFVALGTVIRGETYHFDIVSNESCRALTDLSVEESIAIGNGILTVENEEQAWVRARREDKDKGGFAARAALTMIGLRKKFGA 157
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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  (0, 0)

(no "SCOP Domain" information available for 2O6H)

(-) 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  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RISB1_BRUME | Q8YGH2)
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: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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 Related Entries

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(-) Related Entries Specified in the PDB File

2f59 LUMAZINE SYNTHASE RIBH1 FROM BRUCELLA ABORTUS (GENE BRUAB1_ 0785, SWISS-PROT ENTRY Q57DY1) COMPLEXED WITH INHIBITOR 5- NITRO-6-(D-RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE