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(-) Description

Title :  CRYSTAL STRUCTURE OF 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE OF CANDIDA ALBICANS- ALTERNATE INTERPRETATION
 
Authors :  R. E. Stenkamp, I. Le Trong
Date :  12 Oct 07  (Deposition) - 29 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alternate Model, Magnesium, Manganese, Metal-Binding, Riboflavin Biosynthesis, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Le Trong, R. E. Stenkamp
Alternative Models For Two Crystal Structures Of Candida Albicans 3, 4-Dihydroxy-2-Butanone 4-Phosphate Synthase.
Acta Crystallogr. , Sect. D V. 64 219 2008
PubMed-ID: 18219123  |  Reference-DOI: 10.1107/S0907444907056132
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO-CARIB3-SYN
    Expression System Strain: XL1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIB3
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:125 -Pro A:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:196
 aligned with RIB3_CANAL | Q5A3V6 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:202
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  
           RIB3_CANAL     3 NIFTPIEEALEAYKNGEFLIVMDDEDRENEGDLIMAAELITQEKMAFLVRYSSGYVCVPLSEERANQLELPPMLANRSDRHGTAYTITCDFAEGTTTGISAHDRALTTRSLANPNSKPQDFIKPGHILPLRAVPGLLKKRRGHTEAAVQLSTLAGLQPAGVICELVRDEDGLMMRLDDCIQFGKKHGIKIININQLVEYISK 204
               SCOP domains d2risa_ A: automated matches                                                                                                                                                                               SCOP domains
               CATH domains 2risA00 A:3-204 DHBP synthase                                                                                                                                                                              CATH domains
               Pfam domains -----DHBP_synthase-2risA01 A:8-202                                                                                                                                                                      -- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...eeee.........eeeee.hhhhhhhhhhhhhh.....eeeeehhhhhhh.......------.......eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhh.....eeeee..........hhhhhhhhhhhhh.eeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ris A   3 NIFTPIEEALEAYKNGEFLIVMDDEDRENEGDLIMAAELITQEKMAFLVRYSSGYVCVPLSEERANQLELPPMLA------GTAYTITCDFAEGTTTGISAHDRALTTRSLANPNSKPQDFIKPGHILPLRAVPGLLKKRRGHTEAAVQLSTLAGLQPAGVICELVRDEDGLMMRLDDCIQFGKKHGIKIININQLVEYISK 204
                                    12        22        32        42        52        62        72    |    - |      92       102       112       122       132       142       152       162       172       182       192       202  
                                                                                                     77     84
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  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  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIB3_CANAL | Q5A3V6)
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).

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    Lys A:125 - Pro A:126   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIB3_CANAL | Q5A3V6: 1tks 1tku 2riu

(-) Related Entries Specified in the PDB File

1tks THE DATA SET FROM 1TKS WAS REINDEXED AND USED FOR REFINEMENT OF A MONOCLINIC MODEL.
2riu