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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE IN COMPLEX WITH SULFATE ION.
 
Authors :  P. Kumar, S. Karthikeyan
Date :  11 Feb 10  (Deposition) - 15 Sep 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Enzyme-Sulfate Complex, Alpha+Beta Barrel, Drug Target, Antibacterial, Lyase, Metal-Binding, Riboflavin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kumar, M. Singh, R. Gautam, S. Karthikeyan
Potential Anti-Bacterial Drug Target: Structural Characterization Of 3, 4-Dihydroxy-2-Butanone-4-Phosphate Synthase From Salmonella Typhimurium Lt2.
Proteins V. 78 3292 2010
PubMed-ID: 20806221  |  Reference-DOI: 10.1002/PROT.22837

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.1.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIBB, STM3195
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 90371
    Strain: LT2
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:93 , ARG A:150 , GLY A:152 , HIS A:153 , THR A:154BINDING SITE FOR RESIDUE SO4 A 303
2AC2SOFTWAREALA A:190BINDING SITE FOR RESIDUE SO4 A 304
3AC3SOFTWAREARG B:150 , GLY B:152 , HIS B:153 , THR B:154BINDING SITE FOR RESIDUE SO4 B 302
4AC4SOFTWARETHR C:93 , ARG C:150 , GLY C:152 , HIS C:153 , THR C:154BINDING SITE FOR RESIDUE SO4 C 300
5AC5SOFTWAREGLU A:85 , GLU C:72 , ARG C:141 , GLN C:143 , ALA C:144BINDING SITE FOR RESIDUE SO4 C 305
6AC6SOFTWAREGLU D:38 , THR D:93 , ARG D:150 , GLY D:152 , HIS D:153 , THR D:154BINDING SITE FOR RESIDUE SO4 D 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LRJ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:133 -Pro A:134
2Arg B:133 -Pro B:134
3Arg C:133 -Pro C:134
4Arg D:133 -Pro D:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LRJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LRJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3LRJ)

(-) 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:199
 aligned with RIBB_SALTY | P66032 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:204
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
           RIBB_SALTY     9 FGTPFERVELALDALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
               SCOP domains d3lrja_ A: automated matc     hes                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...eeee.-----...eeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lrj A   9 FGTPFERVELALDALREGRGVMVLD-----NEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
                                    18        28    |    -|       48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
                                                   33    39                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with RIBB_SALTY | P66032 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:202
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           RIBB_SALTY    11 TPFERVELALDALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
               SCOP domains d3lrjb_ B: automated mat    ches                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...eeee..----...eeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrj B  11 TPFERVELALDALREGRGVMVLDD----NEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
                                    20        30   |    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
                                                  34   39                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:198
 aligned with RIBB_SALTY | P66032 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:204
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
           RIBB_SALTY     9 FGTPFERVELALDALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
               SCOP domains d3lrjc_ C: automated matc      hes                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...eeee.------..eeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lrj C   9 FGTPFERVELALDALREGRGVMVLD------EGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
                                    18        28    |    - |      48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    
                                                   33     40                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:199
 aligned with RIBB_SALTY | P66032 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:202
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           RIBB_SALTY    11 TPFERVELALDALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
               SCOP domains d3lrjd_ D: automated mat   ches                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DHBP_synthase-3lrjD   01 D:16-209                                                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) -----DHBP_synthase-3lrjD   02 D:16-209                                                                                                                                                                 --- Pfam domains (2)
           Pfam domains (3) -----DHBP_synthase-3lrjD   03 D:16-209                                                                                                                                                                 --- Pfam domains (3)
           Pfam domains (4) -----DHBP_synthase-3lrjD   04 D:16-209                                                                                                                                                                 --- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhh...eeee..---...eeeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhh...eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrj D  11 TPFERVELALDALREGRGVMVLDD---ENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
                                    20        30   |   |40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
                                                  34  38
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LRJ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHBP_synthase] (17)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RIBB_SALTY | P66032)
molecular function
    GO:0008686    3,4-dihydroxy-2-butanone-4-phosphate synthase activity    Catalysis of the reaction: D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate + formate + H(+).
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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).

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  4.1.99.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBB_SALTY | P66032: 3lqu 3ls6

(-) Related Entries Specified in the PDB File

3lqu CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE4-PHOSPHATE IN COMPLEX WITH RIBULOSE5-PHOSPHATE