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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE (CATION FREE FORM)
 
Authors :  D. -I. Liao, Y. -J. Zheng, P. V. Viitanen, D. B. Jordan
Date :  06 Oct 01  (Deposition) - 06 Mar 02  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dihydroxybutanone Phosphate Synthase, Riboflavin Biosynthesis, Antimicrobial Target, Structure-Based Design, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. I. Liao, Y. J. Zheng, P. V. Viitanen, D. B. Jordan
Structural Definition Of The Active Site And Catalytic Mechanism Of 3, 4-Dihydroxy-2-Butanone-4-Phosphate Synthase.
Biochemistry V. 41 1795 2002
PubMed-ID: 11827524  |  Reference-DOI: 10.1021/BI015652U

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-24A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RICE BLAST FUNGI
    Organism Scientific: MAGNAPORTHE GRISEA
    Organism Taxid: 148305

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , THR A:92 , ARG A:150 , GLY A:152 , HIS A:153 , THR A:154 , HOH A:1112 , HOH A:1161BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREGLN A:81 , ARG A:141 , ARG A:205 , HOH A:1080 , HOH A:1085 , HOH A:1175BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREGLY A:192 , MET A:193 , ARG A:195 , HOH A:1070BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREARG A:59 , ARG A:188 , HOH A:1014 , HOH A:1090 , HOH A:1135 , HOH A:1174 , HOH A:1224BINDING SITE FOR RESIDUE SO4 A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K49)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:133 -Pro A:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K49)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K49)

(-) Exons   (0, 0)

(no "Exon" information available for 1K49)

(-) 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:208
 aligned with RIB3_MAGO7 | Q8TG90 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:215
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
           RIB3_MAGO7    11 NFDAIPDVIQAFKNGEFVVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERTTALDLPQMVTHNADPRGTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRPGHVFPLRAVAGGVRARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGMLRGDECVAFARRWGLKVCTIEDMIAHVEKTEG 225
               SCOP domains d1k49a_ A: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase,        RibB                                                                                                                                    SCOP domains
               CATH domains 1k49A00 A:11-225 DHBP synthase                                                                                                                                                                                          CATH domains
               Pfam domains ----DHBP_synthase-1k49A01 A:15-220                                                                                                                                                                                ----- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh...eeee........eeeeee....hhhhhhhhhhh.....eeeehhhhhhhhh.....-------.......eee.........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee.ee..............ee.hhhhhhhhhhhh..eeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k49 A  11 NFDAIPDVIQAFKNGEFVVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERTTALDLPQMV-------GTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRPGHVFPLRAVAGGVRARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGMLRGDECVAFARRWGLKVCTIEDMIAHVEKTEG 225
                                    20        30        40        50        60        70        80  |      -|      100       110       120       130       140       150       160       170       180       190       200       210       220     
                                                                                                   83      91
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIB3_MAGO7 | Q8TG90)
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: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:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIB3_MAGO7 | Q8TG90: 1k4i 1k4l 1k4o 1k4p

(-) Related Entries Specified in the PDB File

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