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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF TRIMERIC RIBOFLAVIN SYNTHASE FROM BRUCELLA ABORTUS IN COMPLEX WITH 5-NITRO-6-(D-RIBITYLAMINO)-2,4(1H, 3H) PYRIMIDINEDIONE
 
Authors :  M. I. Serer, H. R. Bonomi, B. G. Guimaraes, R. C. Rossi, F. A. Goldbaum, S.
Date :  23 Aug 12  (Deposition) - 12 Mar 14  (Release) - 28 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Transferase, Beta Barrel, Alpha + Beta Protein, Riboflavin Biosynthesis (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: 469008
    Expression System Vector Type: PLASMID
    Gene: BAA13334_I02741, 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, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1INI6Mod. Residue5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:46 , CYS A:47 , LEU A:48 , THR A:49 , GLU A:66 , ALA A:67 , TRP A:68 , GLU A:70 , GLY A:105 , HIS A:106 , VAL A:107 , HOH A:439 , HOH A:443 , LYS B:140 , ILE B:165 , INI B:302 , HOH B:426BINDING SITE FOR RESIDUE INI A 301
2AC2SOFTWAREGLY A:4 , ILE A:5 , ILE A:6 , THR A:148 , SER A:149 , LEU A:150 , THR A:151 , LEU A:163 , LEU A:164 , ILE A:165 , SER A:168 , VAL A:171 , THR A:172 , HOH A:456 , HOH A:467 , HOH A:492BINDING SITE FOR RESIDUE INI A 302
3AC3SOFTWAREVAL B:46 , CYS B:47 , LEU B:48 , THR B:49 , GLU B:66 , ALA B:67 , TRP B:68 , GLU B:70 , ALA B:71 , LEU B:74 , GLY B:105 , HIS B:106 , VAL B:107 , HOH B:452 , HOH B:454BINDING SITE FOR RESIDUE INI B 301
4AC4SOFTWAREINI A:301 , GLY B:4 , ILE B:5 , ILE B:6 , THR B:148 , SER B:149 , LEU B:150 , THR B:151 , LEU B:163 , LEU B:164 , ILE B:165 , HIS B:167 , SER B:168 , VAL B:171 , THR B:172 , HOH B:414 , HOH B:427 , HOH B:457BINDING SITE FOR RESIDUE INI B 302
5AC5SOFTWAREVAL C:46 , CYS C:47 , LEU C:48 , THR C:49 , GLU C:66 , ALA C:67 , TRP C:68 , GLU C:70 , ALA C:71 , GLY C:105 , HIS C:106 , VAL C:107 , HOH C:461 , HOH C:474BINDING SITE FOR RESIDUE INI C 301
6AC6SOFTWAREGLY C:4 , ILE C:5 , ILE C:6 , THR C:148 , SER C:149 , LEU C:150 , THR C:151 , LEU C:163 , LEU C:164 , ILE C:165 , HIS C:167 , SER C:168 , VAL C:171 , THR C:172 , HOH C:451 , HOH C:452 , HOH C:491 , HOH C:492BINDING SITE FOR RESIDUE INI C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GQN)

(-) Exons   (0, 0)

(no "Exon" information available for 4GQN)

(-) 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
                                                                                                                                                                                                                                        
               SCOP domains d4gqna1 A:1-96 automated matches                                                                d4gqna2 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..................eeeeeeeeeee..eeeeeee.hhhhh.......eeee..eeee...ee..eeeeeehhhhhhhhhhhhh....eeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqn 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:205
                                                                                                                                                                                                                                             
               SCOP domains d4gqnb1 B:1-96 automated matches                                                                d4gqnb2 B:97-205 automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee...hhhhh....eeee..eeeeeee.........eeeeeeehhhhhhhhhhhh....eeeeee..................eeeeeeeeeee..eeeeeee....hhhhh....eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqn B   1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQYQKLEH 205
                                    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:200
                                                                                                                                                                                                                                        
               SCOP domains d4gqnc1 C:1-96 automated matches                                                                d4gqnc2 C:97-200 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeee...hhhhh....eeee..eeeeeee.........eeeeeehhhhhhhhhhhhh....eeeeee..................eeeeeeeeeee..eeeeeee....hhhhh....eeee..eeeeeeeee..eeeeeehhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gqn C   1 MFTGIITDIGKVDRVKPLNEGVLLRIETAYDPETIELGASIACSGVCLTVVALPEKGSNARWFEVEAWEEALRLTTISSWQSGRKINLERSLKLGDEMGGHLVFGHVDGQAEIVERKDEGDAVRFTLRAPEELAPFIAQKGSVALDGTSLTVNGVNANEFDVLLIRHSLEVTTWGERKAGDKVNIEIDQLARYAARLAQY 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 6)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RISA_BRUA2 | Q2YN92: 4e0f 4fxu 4g6i

(-) Related Entries Specified in the PDB File

1i8d THE SAME ENZYME FROM ESCHERICHIA COLI
1kzl THE SAME ENZYME FROM SCHIZOSACCHAROMYCES POMBE
4e0f THE SAME PROTEIN WITH BOUND RIBOFLAVIN
4fxu THE SAME PROTEIN WITHOUT LIGANDS (APO FORM)
4g6i THE SAME PROTEIN WITH BOUND ROSEOFLAVIN