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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE IN COMPLEX WITH ONE MANGANESE, AND A GLYCEROL
 
Authors :  D. -I. Liao, Y. -J. Zheng, P. V. Viitanen, D. B. Jordan
Date :  08 Oct 01  (Deposition) - 06 Mar 02  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
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  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MN1Ligand/IonMANGANESE (II) ION
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN-1Ligand/IonMANGANESE (II) ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , GLU A:37 , THR A:92 , ARG A:150 , GLY A:152 , HIS A:153 , THR A:154 , MN A:1003 , GOL A:1004 , HOH A:1180BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREGLN A:81 , ARG A:141 , ARG A:205 , HOH A:1110 , HOH A:1124BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREGLU A:37 , HIS A:153 , SO4 A:1001 , GOL A:1004 , HOH A:1016BINDING SITE FOR RESIDUE MN A 1003
4AC4SOFTWAREGLU A:37 , ASP A:41 , TYR A:94 , HIS A:136 , HIS A:153 , ILE A:172 , GLU A:174 , SO4 A:1001 , MN A:1003 , HOH A:1016 , HOH A:1048 , HOH A:1102BINDING SITE FOR RESIDUE GOL A 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K4O)

(-) 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 1K4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K4O)

(-) Exons   (0, 0)

(no "Exon" information available for 1K4O)

(-) 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:216
 aligned with RIB3_MAGO7 | Q8TG90 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:216
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      
           RIB3_MAGO7    12 FDAIPDVIQAFKNGEFVVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERTTALDLPQMVTHNADPRGTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRPGHVFPLRAVAGGVRARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGMLRGDECVAFARRWGLKVCTIEDMIAHVEKTEGKL 227
               SCOP domains d1k4oa_ A: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                            SCOP domains
               CATH domains 1k4oA00 A:12-227 DHBP synthase                                                                                                                                                                                           CATH domains
               Pfam domains ---DHBP_synthase-1k4oA01 A:15-220                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhh....................eee.........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhhh.hhhhhhhhhhhhh.....eeeee.ee..ee......ee..ee.hhhhhhhhhhhh..eeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1k4o A  12 FDAIPDVIQAFKNGEFVVVLDDPSRENEADLIIAAESVTTEQMAFMVRHSSGLICAPLTPERTTALDLPQMVTHNADPRGTAYTVSVDAEHPSTTTGISAHDRALACRMLAAPDAQPSHFRRPGHVFPLRAVAGGVRARRGHTEAGVELCRLAGKRPVAVISEIVDDGQEVEGRAVRAAPGMLRGDECVAFARRWGLKVCTIEDMIAHVEKTEGKL 227
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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: 1k49 1k4i 1k4l 1k4p

(-) Related Entries Specified in the PDB File

1k49 SAME ENZYME BUT NO CATION IN THE ACTIVE SITE
1k4i SAME ENZYME BUT WITH TWO MG++ IONS IN THE ACTIVE SITE
1k4l SAME ENZYME BUT WITH TWO MN++ ION IN THE ACTIVE SITE