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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
 
Authors :  D. -I. Liao, J. C. Calabrese, Z. Wawrzak, P. V. Viitanen, D. B. Jordan
Date :  30 Oct 00  (Deposition) - 30 Apr 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dihydroxybutanone Phosphate Synthase, Riboflavine Biosynthesis, Skeletal Rearrangement, Antimicrobial Target, Structure-Based Design, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. I. Liao, J. C. Calabrese, Z. Wawrzak, P. V. Viitanen, D. B. Jordan
Crystal Structure Of 3, 4-Dihydroxy-2-Butanone 4-Phosphate Synthase Of Riboflavin Biosynthesis.
Structure V. 9 11 2001
PubMed-ID: 11342130  |  Reference-DOI: 10.1016/S0969-2126(00)00550-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24D(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CS4Ligand/IonCESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:59 , ARG A:60 , GLY A:62 , HOH A:506 , HOH A:582 , ILE B:59 , CS B:502BINDING SITE FOR RESIDUE CS A 501
2AC2SOFTWAREILE A:59 , CS A:501 , HOH A:506 , ILE B:59 , ARG B:60 , GLY B:62 , HOH B:564BINDING SITE FOR RESIDUE CS B 502
3AC3SOFTWAREALA A:164 , GLY A:165 , PHE A:166 , HOH A:555 , HOH A:620 , HOH A:624BINDING SITE FOR RESIDUE CS A 503
4AC4SOFTWAREGLU A:48 , ARG A:119 , HOH A:548 , HOH A:562 , HOH A:628BINDING SITE FOR RESIDUE CS A 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G57)

(-) 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 1G57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G57)

(-) Exons   (0, 0)

(no "Exon" information available for 1G57)

(-) 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_ECOLI | P0A7J0 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:209
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
           RIBB_ECOLI     5 LLSSFGTPFERVENALAALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIEFANKHNMALVTIEDLVAYRQAHE 213
               SCOP domains d1g57a_ A: 3,4-dihydroxy-2-bu    tanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                 SCOP domains
               CATH domains 1g57A00 A:5-213 DHBP synthase                                                                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh...eeeee----..eeeeeee....hhhhhhhhhhhh....eeeehhhhhhhh....................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhh..eeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g57 A   5 LLSSFGTPFERVENALAALREGRGVMVLD----ENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIEFANKHNMALVTIEDLVAYRQAHE 213
                                    14        24        |-   |    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                       33   38                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with RIBB_ECOLI | P0A7J0 from UniProtKB/Swiss-Prot  Length:217

    Alignment length:214
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
           RIBB_ECOLI     4 TLLSSFGTPFERVENALAALREGRGVMVLDDEDRENEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIEFANKHNMALVTIEDLVAYRQAHERKAS 217
               SCOP domains d1g57b_ B: 3,4-dihydroxy-2-but     anone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                     SCOP domains
               CATH domains 1g57B00 B:4-217 DHBP synthase                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...eeee.-----..eeeeee....hhhhhhhhhhhh....eeeehhhhhhhhh...................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhh..eeeehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g57 B   4 TLLSSFGTPFERVENALAALREGRGVMVLD-----NEGDMIFPAETMTVEQMALTIRHGSGIVCLCITEDRRKQLDLPMMVENNTSAYGTGFTVTIEAAEGVTTGVSAADRITTVRAAIADGAKPSDLNRPGHVFPLRAQAGGVLTRGGHTEATIDLMTLAGFKPAGVLCELTNDDGTMARAPECIEFANKHNMALVTIEDLVAYRQAHERKAS 217
                                    13        23        33     |  43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                        33    39
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G57)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RIBB_ECOLI | P0A7J0)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

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        RIBB_ECOLI | P0A7J0: 1g58 1iez

(-) Related Entries Specified in the PDB File

1g58 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE GOLD DERIVATIVE