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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ARCHAEAL PENTAMERIC RIBOFLAVIN SYNTHASE COMPLEX WITH A SUBSTRATE ANALOG INHIBITOR
 
Authors :  A. Ramsperger, M. Augustin, A. K. Schott, S. Gerhardt, T. Krojer, W. Eisenreich, B. Illarionov, M. Cushman, A. Bacher, R. Huber, M. Fischer
Date :  11 Oct 05  (Deposition) - 08 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Lumazine Riboflavin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ramsperger, M. Augustin, A. K. Schott, S. Gerhardt, T. Krojer, W. Eisenreich, B. Illarionov, M. Cushman, A. Bacher, R. Huber, M. Fischer
Crystal Structure Of An Archaeal Pentameric Riboflavin Synthase In Complex With A Substrate Analog Inhibitor: Stereochemical Implications
J. Biol. Chem. V. 281 1224 2006
PubMed-ID: 16272154  |  Reference-DOI: 10.1074/JBC.M509440200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOFLAVIN SYNTHASE
    Chains: A, B, C, D, E
    EC Number: 2.5.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO113
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RIBOFLAVIN SYNTHASE
    Gene: RIBC
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1RDL10Ligand/Ion6,7-DIOXO-5H-8-RIBITYLAMINOLUMAZINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE C:12 , GLY C:41 , ILE C:42 , LYS C:43 , ASP C:44 , MET C:66 , PRO C:67 , GLY C:68 , ASP C:73 , CYS C:76 , HOH C:1217 , ILE E:96 , GLU E:97 , HIS E:122 , RDL E:1202BINDING SITE FOR RESIDUE RDL C 1201
2AC2SOFTWAREPHE C:12 , ASP C:73 , RDL C:1201 , PHE E:99 , ARG E:118 , HIS E:122 , ARG E:145 , GLN E:146BINDING SITE FOR RESIDUE RDL E 1202
3AC3SOFTWAREILE C:96 , GLU C:97 , HIS C:122 , GLN C:146 , RDL C:1204 , PHE D:12 , PRO D:40 , GLY D:41 , ILE D:42 , LYS D:43 , ASP D:44 , MET D:66 , PRO D:67 , GLY D:68 , ASP D:73 , CYS D:76 , HOH D:1204 , HOH D:1208 , HOH D:1209BINDING SITE FOR RESIDUE RDL D 1203
4AC4SOFTWAREPHE C:99 , HIS C:101 , ARG C:118 , HIS C:122 , ARG C:145 , GLN C:146 , HOH C:1205 , ASP D:73 , RDL D:1203BINDING SITE FOR RESIDUE RDL C 1204
5AC5SOFTWAREPHE A:12 , GLY A:41 , ILE A:42 , LYS A:43 , ASP A:44 , MET A:66 , PRO A:67 , GLY A:68 , ASP A:73 , CYS A:76 , HOH A:1223 , ILE B:96 , GLU B:97 , HIS B:122BINDING SITE FOR RESIDUE RDL A 1205
6AC6SOFTWAREILE A:96 , GLU A:97 , HIS A:122 , RDL A:1208 , PHE E:12 , GLY E:41 , ILE E:42 , LYS E:43 , ASP E:44 , MET E:66 , PRO E:67 , GLY E:68 , ASP E:73 , CYS E:76 , HOH E:1216BINDING SITE FOR RESIDUE RDL E 1207
7AC7SOFTWAREPHE A:99 , GLU A:104 , ARG A:118 , HIS A:122 , ARG A:145 , PHE E:12 , ASP E:73 , RDL E:1207BINDING SITE FOR RESIDUE RDL A 1208
8AC8SOFTWAREPHE B:12 , ASP B:73 , RDL B:1210 , PHE D:99 , GLU D:104 , ARG D:118 , HIS D:122BINDING SITE FOR RESIDUE RDL B 1209
9AC9SOFTWAREPHE B:12 , GLY B:41 , ILE B:42 , LYS B:43 , ASP B:44 , MET B:66 , PRO B:67 , GLY B:68 , ASP B:73 , CYS B:76 , RDL B:1209 , HOH B:1222 , ILE D:96 , GLU D:97 , HIS D:122BINDING SITE FOR RESIDUE RDL B 1210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B99)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B99)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B99)

(-) Exons   (0, 0)

(no "Exon" information available for 2B99)

(-) 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:146
 aligned with RISC_METJA | Q58584 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:146
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      
           RISC_METJA     2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGLRQG 147
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b99 A   2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGLRQG 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with RISC_METJA | Q58584 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:143
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   
           RISC_METJA     2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGL 144
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b99 B   2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGL 144
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   


Chain C from PDB  Type:PROTEIN  Length:152
 aligned with RISC_METJA | Q58584 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           RISC_METJA     2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGLRQGFEDAGP 153
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b99 C   2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGLRQGFEDAGP 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  


Chain D from PDB  Type:PROTEIN  Length:141
 aligned with RISC_METJA | Q58584 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:141
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142 
           RISC_METJA     3 KKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKG 143
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b99 D   3 KKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKG 143
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142 


Chain E from PDB  Type:PROTEIN  Length:152
 aligned with RISC_METJA | Q58584 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:152
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151  
           RISC_METJA     2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGLRQGFEDAGP 153
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b99 E   2 TKKVGIVDTTFARVDMASIAIKKLKELSPNIKIIRKTVPGIKDLPVACKKLLEEEGCDIVMALGMPGKAEKDKVCAHEASLGLMLAQLMTNKHIIEVFVHEDEAKDDKELDWLAKRRAEEHAENVYYLLFKPEYLTRMAGKGLRQGFEDAGP 153
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151
   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 2B99)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B99)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (RISC_METJA | Q58584)
molecular function
    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: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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  2b99
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 Related Entries

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

UniProtKB/Swiss-Prot
        RISC_METJA | Q58584: 2b98 4y7j 4y7k 5im5

(-) Related Entries Specified in the PDB File

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