PDBsum entry 1snn

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
Protein chains
219 a.a. *
5RP ×2
_ZN ×3
_CA ×4
Waters ×352
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: 3,4-dihydroxy-2-butanone 4-phosphate synthase from methanococcus jannaschii
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)
1.55Å     R-factor:   0.200     R-free:   0.234
Authors: S.Steinbacher,S.Schiffmann,R.Huber,A.Bacher,M.Fischer
Key ref:
S.Steinbacher et al. (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. PubMed id: 15213409 DOI: 10.1107/S0907444904009862
11-Mar-04     Release date:   20-Jul-04    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 219 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - 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  


DOI no: 10.1107/S0907444904009862 Acta Crystallogr D Biol Crystallogr 60:1338-1340 (2004)
PubMed id: 15213409  
Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate.
S.Steinbacher, S.Schiffmann, A.Bacher, M.Fischer.
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 centre has recently been determined at 1.7 A resolution. The enzyme converts ribulose 5-phosphate into 3,4-dihydroxy-2-butanone 4-phosphate, while its C4 atom is released as formate. The resulting four-carbon body supplies all eight C atoms for the xylene moiety of riboflavin. Three of the four hydroxyl groups of ribulose 5-phosphate were coordinated by the metal ions. Based on crystallographic refinement, the metals were assigned as zinc and calcium, which were present in the crystallization buffer. Neither metal supports the enzymatic reaction. In the present study, the correctness of this assignment is assessed using anomalous diffraction data collected at the high-energy side of the zinc absorption edge (lambda = 1.2823 A). Only the three tentative zinc ions give strong peaks in an anomalous difference Fourier map (>20sigma), whereas the four tentative calcium ions do not show anomalous signals above the noise level. These results confirm the initial assignment. In addition, the resolution was improved to 1.55 A.
  Selected figure(s)  
Figure 1.
Figure 1 Ribbon diagram of the M. jannaschii DHBPS (Steinbacher et al., 2003[Steinbacher, S., Schiffmann, S., Richter, G., Huber, R., Bacher, A. & Fischer, M. (2003). J. Biol. Chem. 278, 42256-42265.]) dimer. Calcium and zinc ions are shown as grey and red balls, respectively. The bound substrate Ru5P is depicted as a blue ball-and-stick model and the acidic loop is in purple.
  The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1338-1340) copyright 2004.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
16010344 M.Fischer, and A.Bacher (2005).
Biosynthesis of flavocoenzymes.
  Nat Prod Rep, 22, 324-350.  
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