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(-) Description

Title :  3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE FROM M. JANNASCHII IN COMPLEX WITH RIBULOSE 5-PHOSPHATE
 
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 :  1.70
Chains :  Asym./Biol. Unit :  A,B
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
    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
    Mutation: YES
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
15RP2Ligand/IonRIBULOSE-5-PHOSPHATE
2CA4Ligand/IonCALCIUM ION
3ZN3Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:25 , GLU A:26 , ASP A:30 , CYS A:55 , TYR A:95 , LEU A:151 , ARG A:161 , GLY A:163 , HIS A:164 , THR A:165 , ILE A:183 , GLU A:185 , ZN A:502 , CA A:503 , HOH A:723 , HOH A:766 , HOH A:847 , HOH A:851 , HOH A:852BINDING SITE FOR RESIDUE 5RP A 501
2AC2SOFTWAREARG B:25 , GLU B:26 , ASP B:30 , CYS B:55 , PHE B:101 , ARG B:161 , GLY B:163 , HIS B:164 , THR B:165 , GLU B:185 , ZN B:602 , CA B:603 , HOH B:772 , HOH B:778 , HOH B:785 , HOH B:804 , HOH B:805 , HOH B:806BINDING SITE FOR RESIDUE 5RP B 601
3AC3SOFTWAREGLU A:26 , HIS A:164 , 5RP A:501 , HOH A:852BINDING SITE FOR RESIDUE ZN A 502
4AC4SOFTWAREGLU A:26 , TYR A:95 , 5RP A:501 , HOH A:851BINDING SITE FOR RESIDUE CA A 503
5AC5SOFTWAREGLU B:26 , HIS B:164 , 5RP B:601 , HOH B:805BINDING SITE FOR RESIDUE ZN B 602
6AC6SOFTWAREGLU B:26 , 5RP B:601 , HOH B:764 , HOH B:804 , HOH B:806BINDING SITE FOR RESIDUE CA B 603
7AC7SOFTWAREASP A:96 , GLU A:97 , HOH A:753 , HOH A:769 , HOH A:774 , HOH A:806BINDING SITE FOR RESIDUE CA A 701
8AC8SOFTWAREGLU A:204 , ASN A:207 , HOH A:787 , HOH B:613 , HOH B:655BINDING SITE FOR RESIDUE CA A 702
9AC9SOFTWAREHIS A:206BINDING SITE FOR RESIDUE ZN A 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:144 -Pro A:145
2Ser B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PVY)

(-) 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: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 d1pvya_ A: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                               SCOP domains
               CATH domains 1pvyA00 A:2-220 DHBP synthase                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhheeeeeeeehhhhhhhhh..hhhhhhhhhh..hhhhhh.............eeeeeee.......hhhhhhhhhhhhhhhhhh.hhhhhhhheeeeeeeeeee...hhhhh..hhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhh...eeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvy A   2 NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGSVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYY 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
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
           RIBB_METJA     3 NVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGHVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYYL 221
               SCOP domains d1pvyb_ B: 3,4-dihydroxy-2-butanone 4-phosphate synthase, DHBP synthase, RibB                                                                                                                                               SCOP domains
               CATH domains 1pvyB00 B:3-221 DHBP synthase                                                                                                                                                                                               CATH domains
           Pfam domains (1) -DHBP_synthase-1pvyB01 B:4-220                                                                                                                                                                                            - Pfam domains (1)
           Pfam domains (2) -DHBP_synthase-1pvyB02 B:4-220                                                                                                                                                                                            - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhheeeeeeeehhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee...hhhhh..hhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhh...eeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvy B   3 NVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAGGLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSFSITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGSVTLLRAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKRYAEKHNLIYLSGEEIINYYL 221
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212
   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  (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_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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1pvw 1PVW CONTAINS 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE.