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PDBsum entry 1fui

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protein ligands metals Protein-protein interface(s) links
Isomerase PDB id
1fui
Jmol
Contents
Protein chains
(+ 0 more) 591 a.a. *
Ligands
SO4 ×2
FOC ×6
Metals
_MN ×5
Waters ×872
* Residue conservation analysis
PDB id:
1fui
Name: Isomerase
Title: L-fucose isomerase from escherichia coli
Structure: L-fucose isomerase. Chain: a, b, c, d, e, f. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cell_line: jm105. Cellular_location: cytoplasm. Gene: fuci. Expressed in: escherichia coli k12. Expression_system_taxid: 83333. Expression_system_cell_line: jm105.
Biol. unit: Trimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.162     R-free:   0.209
Authors: J.E.Seemann,G.E.Schulz
Key ref:
J.E.Seemann and G.E.Schulz (1997). Structure and mechanism of L-fucose isomerase from Escherichia coli. J Mol Biol, 273, 256-268. PubMed id: 9367760 DOI: 10.1006/jmbi.1997.1280
Date:
14-Apr-97     Release date:   15-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P69922  (FUCI_ECOLI) -  L-fucose isomerase
Seq:
Struc:
 
Seq:
Struc:
591 a.a.
591 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.5.3.1.25  - L-fucose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-fucopyranose = L-fuculose
L-fucopyranose
Bound ligand (Het Group name = FOC)
corresponds exactly
= L-fuculose
      Cofactor: Mn(2+)
   Enzyme class 3: E.C.5.3.1.3  - D-arabinose isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-arabinose = D-ribulose
D-arabinose
= D-ribulose
      Cofactor: Mn(2+)
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     carbohydrate metabolic process   6 terms 
  Biochemical function     isomerase activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1997.1280 J Mol Biol 273:256-268 (1997)
PubMed id: 9367760  
 
 
Structure and mechanism of L-fucose isomerase from Escherichia coli.
J.E.Seemann, G.E.Schulz.
 
  ABSTRACT  
 
The three-dimensional structure of L-fucose isomerase from Escherichia coli has been determined by X-ray crystallography at 2.5 A resolution. This ketol isomerase converts the aldose L-fucose into the corresponding ketose L-fuculose using Mn2+ as a cofactor. Being a hexamer with 64,976 Da per subunit, L-fucose isomerase is the largest structurally known ketol isomerase. The enzyme shows neither sequence nor structural similarity with other ketol isomerases. The hexamer obeys D3 symmetry and forms the crystallographic asymmetric unit. The strict and favorably oriented local symmetry allowed for a computational phase extension from 7.3 A to 2.5 A resolution. The structure was solved with an L-fucitol molecule bound to the catalytic center such that the hydroxyl groups at positions 1 and 2 are ligands of the manganese ion. Most likely, L-fucitol mimics a bound L-fucose molecule in its open chain form. The protein environment suggests strongly that the reaction belongs to the ene-diol type.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Topology sketch of FucIase. Circles correspond to a-helices and squares to b-strands, concentric squares indicate b-strands running away from the viewer. The two residue numbers mark the domain borders. Three short helices and seven b-strands were omitted for clarity. Three of the omitted b-strands (b8, b17, and b18) form a separate mixed sheet, b10 and b11 as well as b15 and b16 form local hair-pins. All omitted secondary structures can be viewed in Figure 4(b).
Figure 11.
Figure 11. Scheme of the reaction catalyzed by FucIase. The isomerization reaction comprises the transfer of two hydrogen atoms (indicated by white arrows). Two types of mechanisms are discussed: in the ene-diol mechan- ism, the two bases Asp A 361 and Glu A 337 transfer the two protons via an ene-diol intermediate. In a hydride- shift mechanism, the hydrogen atom at C2 would migrate as a hydride to C1, and Glu A 337 would be superfluous. The structure indicates an ene-diol mechan- ism for FucIase.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 273, 256-268) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19727704 J.H.Kim, P.Prabhu, M.Jeya, M.K.Tiwari, H.J.Moon, R.K.Singh, and J.K.Lee (2010).
Characterization of an L-arabinose isomerase from Bacillus subtilis.
  Appl Microbiol Biotechnol, 85, 1839-1847.  
20048061 P.Prabhu, M.Jeya, and J.K.Lee (2010).
Probing the molecular determinant for the catalytic efficiency of L-arabinose isomerase from Bacillus licheniformis.
  Appl Environ Microbiol, 76, 1653-1660.  
20406496 Y.Gu, Y.Ding, C.Ren, Z.Sun, D.A.Rodionov, W.Zhang, S.Yang, C.Yang, and W.Jiang (2010).
Reconstruction of xylose utilization pathway and regulons in Firmicutes.
  BMC Genomics, 11, 255.  
  18931442 K.Takeda, H.Yoshida, G.Takada, K.Izumori, and S.Kamitori (2008).
Overexpression, purification, crystallization and preliminary X-ray crystal analysis of Bacillus pallidusD-arabinose isomerase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 945-948.  
18716768 P.Prabhu, M.K.Tiwari, M.Jeya, P.Gunasekaran, I.W.Kim, and J.K.Lee (2008).
Cloning and characterization of a novel L-arabinose isomerase from Bacillus licheniformis.
  Appl Microbiol Biotechnol, 81, 283-290.  
17337581 M.Rhimi, M.Juy, N.Aghajari, R.Haser, and S.Bejar (2007).
Probing the essential catalytic residues and substrate affinity in the thermoactive Bacillus stearothermophilus US100 L-arabinose isomerase by site-directed mutagenesis.
  J Bacteriol, 189, 3556-3563.  
12847518 A.Glasfeld, E.Guedon, J.D.Helmann, and R.G.Brennan (2003).
Structure of the manganese-bound manganese transport regulator of Bacillus subtilis.
  Nat Struct Biol, 10, 652-657.
PDB codes: 1on1 1on2
12829271 D.G.Kehres, and M.E.Maguire (2003).
Emerging themes in manganese transport, biochemistry and pathogenesis in bacteria.
  FEMS Microbiol Rev, 27, 263-290.  
11983887 D.Arsenieva, R.Hardre, L.Salmon, and C.J.Jeffery (2002).
The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid.
  Proc Natl Acad Sci U S A, 99, 5872-5877.
PDB code: 1koj
11976494 M.Kroemer, and G.E.Schulz (2002).
The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging.
  Acta Crystallogr D Biol Crystallogr, 58, 824-832.
PDB code: 1gt7
10089413 C.Vonrhein, and G.E.Schulz (1999).
Locating proper non-crystallographic symmetry in low-resolution electron-density maps with the program GETAX.
  Acta Crystallogr D Biol Crystallogr, 55, 225-229.  
10368289 R.M.Castillo, K.Mizuguchi, V.Dhanaraj, A.Albert, T.L.Blundell, and A.G.Murzin (1999).
A six-stranded double-psi beta barrel is shared by several protein superfamilies.
  Structure, 7, 227-236.  
9739095 A.Teplyakov, G.Obmolova, M.A.Badet-Denisot, B.Badet, and I.Polikarpov (1998).
Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain.
  Structure, 6, 1047-1055.
PDB code: 1moq
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.