8EWU | pdb_00008ewu

X-ray structure of the GDP-6-deoxy-4-keto-D-lyxo-heptose-4-reductase from Campylobacter jejuni HS:15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.219 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Bifunctional Epimerase/Reductase Enzymes Facilitate the Modulation of 6-Deoxy-Heptoses Found in the Capsular Polysaccharides of Campylobacter jejuni.

Xiang, D.F.Ghosh, M.K.Riegert, A.S.Thoden, J.B.Holden, H.M.Raushel, F.M.

(2023) Biochemistry 62: 134-144

  • DOI: https://doi.org/10.1021/acs.biochem.2c00633
  • Primary Citation of Related Structures:  
    8EWU

  • PubMed Abstract: 

    Campylobacter jejuni is a human pathogen and the leading cause of food poisoning in the United States and Europe. Surrounding the exterior surface of this bacterium is a capsular polysaccharide (CPS) that consists of a repeating sequence of common and unusual carbohydrate segments. At least 10 different heptose sugars have thus far been identified in the various strains of C. jejuni . The accepted biosynthetic pathway for the construction of the 6-deoxy-heptoses begins with the 4,6-dehydration of GDP-d- glycero -d- manno -heptose by a dehydratase, followed by an epimerase that racemizes C3 and/or C5 of the product GDP-6-deoxy-4-keto-d- lyxo -heptose. In the final step, a C4-reductase catalyzes the NADPH reduction of the resulting 4-keto product. However, in some strains and serotypes of C. jejuni , there are two separate C4-reductases with different product specificities in the gene cluster for CPS formation. Five pairs of these tandem C4-reductases were isolated, and the catalytic properties were ascertained. In four out of five cases, one of the two C4-reductases is able to catalyze the isomerization of C3 and C5 of GDP-6-deoxy-4-keto-d- lyxo -heptose, in addition to the catalysis of the reduction of C4, thus bypassing the requirement for a separate C3/C5-isomerase. In each case, the 3'-end of the gene for the first C4-reductase contains a poly-G tract of 8-10 guanine residues that may be used to control the expression and/or catalytic activity of either C4-reductase. The three-dimensional structure of the C4-reductase from serotype HS:15, which only does a reduction of C4, was determined to 1.45 Å resolution in the presence of NADPH and GDP.


  • Organizational Affiliation
    • Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GDP-L-fucose synthase
A, B
373Campylobacter jejuniMutation(s): 0 
Gene Names: fclHS15.12
EC: 1.1.1.271
UniProt
Find proteins for F2X7A6 (Campylobacter jejuni subsp. jejuni)
Explore F2X7A6 
Go to UniProtKB:  F2X7A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2X7A6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.219 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.761α = 87.96
b = 56.625β = 81.96
c = 67.38γ = 70.12
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM139428
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122825
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134643

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-01-11
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description