4C20 | pdb_00004c20

L-Fucose Isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.190 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Analysis of Fucose-Processing Enzymes from Streptococcus Pneumoniae.

Higgins, M.A.Suits, M.D.Marsters, C.Boraston, A.B.

(2014) J Mol Biology 426: 1469

  • DOI: https://doi.org/10.1016/j.jmb.2013.12.006
  • Primary Citation Related Structures: 
    4C20, 4C21, 4C22, 4C23, 4C24, 4C25

  • PubMed Abstract: 

    Fucose metabolism pathways are present in many bacterial species and typically contain the central fucose-processing enzymes fucose isomerase (FcsI), fuculose kinase (FcsK), and fuculose-1-phosphate aldolase (FcsA). Fucose initially undergoes isomerization by FcsI producing fuculose, which is then phosphorylated by FcsK. FcsA cleaves the fuculose-1-phosphate product into lactaldehyde and dihydroxyacetone phosphate, which can be incorporated into central metabolism allowing the bacterium to use fucose as an energy source. Streptococcus pneumoniae has fucose-processing operons containing homologs of FcsI, FcsK, and FcsA; however, this bacterium appears unable to utilize fucose as an energy source. To investigate this contradiction, we performed biochemical and structural studies of the S. pneumoniae fucose-processing enzymes SpFcsI, SpFcsK, and SpFcsA. These enzymes are demonstrated to act in a sequential manner to ultimately produce dihydroxyacetone phosphate and have structural features entirely consistent with their observed biochemical activities. Analogous to the regulation of the Escherichia coli fucose utilization operon, fuculose-1-phosphate appears to act as an inducing molecule for activation of the S. pneumoniae fucose operon. Despite our evidence that S. pneumoniae appears to have the appropriate regulatory and biochemical machinery for fucose metabolism, we confirmed the inability of the S. pneumoniae TIGR4 strain to grow on fucose or on the H-disaccharide, which is the probable substrate of the transporter for the pathway. On the basis of these observations, we postulate that the S. pneumoniae fucose-processing pathway has a non-metabolic role in the interaction of this bacterium with its human host.


  • Organizational Affiliation
    • Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, V8W 3P6, Canada.

Macromolecule Content 

  • Total Structure Weight: 136.89 kDa 
  • Atom Count: 10,238 
  • Modeled Residue Count: 1,192 
  • Deposited Residue Count: 1,210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L-FUCOSE ISOMERASE
A, B
605Streptococcus pneumoniae TIGR4Mutation(s): 0 
EC: 5.3.1.25
UniProt
Find proteins for Q97N97 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q97N97 
Go to UniProtKB:  Q97N97
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97N97
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
K [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A],
J [auth A],
R [auth B],
T [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
I [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
C [auth A],
L [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.190 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.931α = 90
b = 151.931β = 90
c = 408.853γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 1.2: 2014-03-19
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description