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PDBsum entry 1pvy

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
1pvy
Jmol
Contents
Protein chains
219 a.a. *
Ligands
5RP ×2
Metals
_ZN ×3
_CA ×4
Waters ×352
* Residue conservation analysis
PDB id:
1pvy
Name: Isomerase
Title: 3,4-dihydroxy-2-butanone 4-phosphate synthase from m. Jannaschii in complex with ribulose 5-phosphate
Structure: 3,4-dihydroxy-2-butanone 4-phosphate synthase. Chain: a, b. Synonym: dhbp synthase. Engineered: yes. Mutation: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: mj0055. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.70Å     R-factor:   0.213     R-free:   0.259
Authors: S.Steinbacher,S.Schiffmann,G.Richter,R.Huber,A.Bacher, M.Fischer
Key ref:
S.Steinbacher et al. (2003). 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, 278, 42256-42265. PubMed id: 12904291 DOI: 10.1074/jbc.M307301200
Date:
29-Jun-03     Release date:   04-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q60364  (RIBB_METJA) -  3,4-dihydroxy-2-butanone 4-phosphate synthase
Seq:
Struc:
227 a.a.
219 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.1.99.12  - 3,4-dihydroxy-2-butanone-4-phosphate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
D-ribulose 5-phosphate
Bound ligand (Het Group name = 5RP)
corresponds exactly
= formate
+ L-3,4-dihydroxybutan-2-one 4-phosphate
      Cofactor: Magnesium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     riboflavin biosynthetic process   1 term 
  Biochemical function     lyase activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M307301200 J Biol Chem 278:42256-42265 (2003)
PubMed id: 12904291  
 
 
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.
S.Steinbacher, S.Schiffmann, G.Richter, R.Huber, A.Bacher, M.Fischer.
 
  ABSTRACT  
 
Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.
 
  Selected figure(s)  
 
Figure 4.
FIG. 4. Comparison of M. jannaschii to M. grisea DBPS (36). a, superposition of the monomers of M. grisea (gold) and M. jannaschii (blue) DBPS in the same orientation as in Fig. 2a. Deviating regions are indicated in pink (M. jannaschii) and purple (M. grisea) for the region around the Tyr-95 loop or light blue for the insertion into the M. jannaschii enzyme, which does not affect the active site. b, superposition of active sites shown that metal I occurs at almost identical positions (Mn2+, turquoise, M. grisea; Zn2+, pink, M. jannaschii). Glycerol and the sulfate ion (blue) bound to M. grisea DBPS superimpose well with bound Ru5P (orange) at metal I.
Figure 6.
FIG. 6. Reactions performed by Rubisco and IspC. a, initial reaction steps of Rubisco. Ribulose 1,5-bisphosphate is converted into an 2,3-enediole that can react with carbon dioxide. Mutants of Rubisco can also undergo -elimination of the 1 phosphate. b, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) introduces the branched isoprenoid skeleton in the mevalonate-independent pathway (left). The complex of IspC with the substrate-like inhibitor fosmidomycin suggests a coordination of the 2-carbonyl and 3-hydroxyl groups of 1-deoxy-D-xylulose 5-phosphate by Mn2+ supporting the 1,2-sigmatropic reaction.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 42256-42265) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21296160 M.Singh, P.Kumar, and S.Karthikeyan (2011).
Structural basis for pH dependent monomer-dimer transition of 3,4-dihydroxy 2-butanone-4-phosphate synthase domain from Mycobacterium tuberculosis.
  J Struct Biol, 174, 374-384.
PDB codes: 3mgz 3mio 3mk5
20430628 A.Talukdar, E.Morgunova, J.Duan, W.Meining, N.Foloppe, L.Nilsson, A.Bacher, B.Illarionov, M.Fischer, R.Ladenstein, and M.Cushman (2010).
Virtual screening, selection and development of a benzindolone structural scaffold for inhibition of lumazine synthase.
  Bioorg Med Chem, 18, 3518-3534.  
20806221 P.Kumar, M.Singh, R.Gautam, and S.Karthikeyan (2010).
Potential anti-bacterial drug target: structural characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella typhimurium LT2.
  Proteins, 78, 3292-3303.
PDB codes: 3lqu 3lrj 3ls6
16010344 M.Fischer, and A.Bacher (2005).
Biosynthesis of flavocoenzymes.
  Nat Prod Rep, 22, 324-350.  
15213409 S.Steinbacher, S.Schiffmann, A.Bacher, and M.Fischer (2004).
Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate.
  Acta Crystallogr D Biol Crystallogr, 60, 1338-1340.
PDB code: 1snn
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.