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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE COMPLEXED WITH RIBULOSE-5 PHOSPHATE
 
Authors :  P. Kumar, S. Karthikeyan
Date :  10 Feb 10  (Deposition) - 15 Sep 10  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dhbps, R5P, Ribb, 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
    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

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15SP1Ligand/Ion5-O-PHOSPHONO-D-XYLULOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:37 , GLU A:38 , GLU A:40 , ILE A:65 , CYS A:67 , THR A:93 , PHE A:95 , ARG A:150 , GLY A:152 , HIS A:153 , THR A:154 , GLU A:174 , HOH A:436 , HIS B:136BINDING SITE FOR RESIDUE 5SP A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:133 -Pro A:134
2Arg B:133 -Pro B:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LQU)

(-) 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:205
 aligned with RIBB_SALTY | P66032 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:205
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207     
           RIBB_SALTY     8 SFGTPFERVELALDALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
               SCOP domains d3lqua_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeee........eeeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhhh.hhhhhhhhhhhhhh....eee...........hhhhhhhhhhhh..eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqu A   8 SFGTPFERVELALDALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207     


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 d3lqub_ B: automated ma    tches                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DHBP_synthase-3lqu    B01 B:16-209                                                                                                                                                                --- Pfam domains (1)
           Pfam domains (2) -----DHBP_synthase-3lqu    B02 B:16-209                                                                                                                                                                --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee.----...eeeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhh.eeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqu B  11 TPFERVELALDALREGRGVMVLD----ENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRVTTVRAAIKDGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIAFAGQHNMAVVTIEDLVAYRQAH 212
                                    20        30  |    |40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
                                                 33   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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