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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF TRIMERIC RIBOFLAVIN SYNTHASE FROM BRUCELLA ABORTUS IN COMPLEX WITH RIBOFLAVIN
 
Authors :  M. I. Serer, H. R. Bonomi, B. G. Guimaraes, R. C. Rossi, F. A. Goldbaum, S.
Date :  03 Mar 12  (Deposition) - 16 Oct 13  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Beta Barrel, Alpha + Beta Protein, Riboflavin Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. I. Serer, H. R. Bonomi, B. G. Guimaraes, R. C. Rossi, F. A. Goldbaum, S. Klinke
Crystallographic And Kinetic Study Of Riboflavin Synthase From Brucella Abortus, A Chemotherapeutic Target With An Enhanced Intrinsic Flexibility.
Acta Crystallogr. , Sect. D V. 70 1419 2014
PubMed-ID: 24816110  |  Reference-DOI: 10.1107/S1399004714005161

(-) Compounds

Molecule 1 - RIBOFLAVIN SYNTHASE SUBUNIT ALPHA
    Chains: A, B, C
    EC Number: 2.5.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIBE
    Organism Scientific: BRUCELLA ABORTUS
    Organism Taxid: 235

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1RBF1Ligand/IonRIBOFLAVIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:40 , VAL A:46 , CYS A:47 , LEU A:48 , THR A:49 , GLU A:66 , ALA A:67 , TRP A:68 , GLU A:70 , ALA A:71 , GLY A:105 , HIS A:106 , VAL A:107 , LYS B:140 , THR B:151 , ILE B:165BINDING SITE FOR RESIDUE RBF A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E0F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4E0F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E0F)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LUMAZINE_BINDPS51177 Riboflavin synthase alpha chain lumazine-binding repeat profile.RISA_BRUA21-101
 
 
102-198
 
 		  6A:1-101
B:1-101
C:1-101
A:102-198
B:102-198
C:102-198

(-) Exons   (0, 0)

(no "Exon" information available for 4E0F)

(-) 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:200
 aligned with RISA_BRUA2 | Q2YN92 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
           RISA_BRUA2     1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQY 200
               SCOP domains d4e0fa1 A:1-96 automated matches                                                                d4e0fa2 A:97-200 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee...hhhhh....eeee..eeeeeee.........eeeeeehhhhhhhhhhhhh....eeeeee.ee...............eeeeeeeeeee..eeeeeee.hhhhh.......eeee..eeee...ee..eeeeeehhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: A:1-101 UniProt: 1-101                                                           LUMAZINE_BIND  PDB: A:102-198 UniProt: 102-198                                                   -- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e0f A   1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQY 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with RISA_BRUA2 | Q2YN92 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:203
                                                                                                                                                                                                                                   202 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 | 
           RISA_BRUA2     1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQYQK-   -
               SCOP domains d4e0fb1 B:1-96 automated matches                                                                d4e0fb2 B:97-203 automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee....eeeeee...hhhhh....eeee..eeeeeee.........eeeeeehhhhhhhhhhhhh....eeeeee......ee..........eeeeeeeeeee..eeeeeee.hhhhhhhh....eeee..eeeeeeeee..eeeeeehhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: B:1-101 UniProt: 1-101                                                           LUMAZINE_BIND  PDB: B:102-198 UniProt: 102-198                                                   ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e0f B   1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQYQKL 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   


Chain C from PDB  Type:PROTEIN  Length:202
 aligned with RISA_BRUA2 | Q2YN92 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
           RISA_BRUA2     1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQYQK 202
               SCOP domains d4e0fc1 C:1-96 automated matches                                                                d4e0fc2 C:97-202 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeeeee...hhhhh....eeee..eeeeeee.........eeeeeeehhhhhhhhhhhh....eeeeee..................eeeeeeeeeee..eeeeeee....hhhhh....eeee..eeeeeeeee..eeeeeehhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE LUMAZINE_BIND  PDB: C:1-101 UniProt: 1-101                                                           LUMAZINE_BIND  PDB: C:102-198 UniProt: 102-198                                                   ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e0f C   1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQYQK 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E0F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E0F)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (RISA_BRUA2 | Q2YN92)
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:1902444    riboflavin binding    Interacting selectively and non-covalently with riboflavin.
    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:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
    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_BRUA2 | Q2YN92: 4fxu 4g6i 4gqn

(-) Related Entries Specified in the PDB File

1i8d THE SAME ENZYME FROM ESCHERICHIA COLI
1kzl THE SAME ENZYME FROM SCHIZOSACCHAROMYCES POMBE