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(-) Description

Title :  3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE FROM M. JANNASCHII
 
Authors :  S. Steinbacher, S. Schiffmann, G. Richter, R. Huber, A. Bacher, M. Fischer
Date :  29 Jun 03  (Deposition) - 04 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  A,B,C  (2x)
Keywords :  Riboflavin Biosynthesis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Steinbacher, S. Schiffmann, G. Richter, R. Huber, A. Bacher, M. Fischer
Structure Of 3, 4-Dihydroxy-2-Butanone 4-Phosphate Synthase From Methanococcus Jannaschii In Complex With Divalent Metal Ions And The Substrate Ribulose 5-Phosphate: Implications For The Catalytic Mechanism
J. Biol. Chem. V. 278 42256 2003
PubMed-ID: 12904291  |  Reference-DOI: 10.1074/JBC.M307301200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A, B, C
    EC Number: 5.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO-MJ
    Expression System Strain: XL1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MJ0055
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C
Biological Unit 3 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2PO41Ligand/IonPHOSPHATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO4-1Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PO42Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:26 , HIS A:164 , CA A:402 , HOH A:403 , HOH A:404 , PO4 A:409BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREGLU A:26 , ZN A:401 , HOH A:404 , HOH A:405 , HOH A:406 , HOH A:408 , PO4 A:409 , HOH B:407BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWAREARG A:25 , GLU A:26 , ARG A:161 , GLY A:163 , HIS A:164 , THR A:165 , ZN A:401 , CA A:402 , HOH A:404 , HOH A:408BINDING SITE FOR RESIDUE PO4 A 409
4AC4SOFTWAREGLU B:128 , GLU B:132 , HIS C:206BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:144 -Pro A:145
2Ser B:144 -Pro B:145
3Ser C:144 -Pro C:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PVW)

(-) 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:219
 aligned with RIBB_METJA | Q60364 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
           RIBB_METJA     2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 220
               SCOP domains d1pvwa_ A: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                               SCOP domains
               CATH domains 1pvwA00 A:2-220 DHBP synthase                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh............eeeeeee.......hhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeeeeee...hhhhh..hhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhh...eeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvw A   2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with RIBB_METJA | Q60364 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
           RIBB_METJA     2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 220
               SCOP domains d1pvwb_ B: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                               SCOP domains
               CATH domains 1pvwB00 B:2-220 DHBP synthase                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...........eeeeeee.......hhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeeeeee...hhhhh..hhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhh...eeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvw B   2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         


Chain C from PDB  Type:PROTEIN  Length:219
 aligned with RIBB_METJA | Q60364 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
           RIBB_METJA     2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 220
               SCOP domains d1pvwc_ C: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                               SCOP domains
               CATH domains 1pvwC00 C:2-220 DHBP synthase                                                                                                                                                                                               CATH domains
           Pfam domains (1) --DHBP_synthase-1pvwC01 C:4-220                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --DHBP_synthase-1pvwC02 C:4-220                                                                                                                                                                                             Pfam domains (2)
           Pfam domains (3) --DHBP_synthase-1pvwC03 C:4-220                                                                                                                                                                                             Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh............eeeeeee.......hhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeeeeee...hhhhh..hhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhh...eeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvw C   2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (RIBB_METJA | Q60364)
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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  5.4.99.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBB_METJA | Q60364: 1pvy 1snn

(-) Related Entries Specified in the PDB File

1pvy 1PVY CONTAINS 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE(H147S) COMPLEXED WITH RIBULOSE 5-PHOSPHATE.