6U7L

2.75 Angstrom Crystal Structure of Galactarate Dehydratase from Escherichia coli.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of galactarate dehydratase, a new fold in an enolase involved in bacterial fitness after antibiotic treatment.

Rosas-Lemus, M.Minasov, G.Shuvalova, L.Wawrzak, Z.Kiryukhina, O.Mih, N.Jaroszewski, L.Palsson, B.Godzik, A.Satchell, K.J.F.

(2020) Protein Sci 29: 711-722

  • DOI: https://doi.org/10.1002/pro.3796
  • Primary Citation of Related Structures:  
    6U7L

  • PubMed Abstract: 

    Galactarate dehydratase (GarD) is the first enzyme in the galactarate/glucarate pathway and catalyzes the dehydration of galactarate to 3-keto-5-dehydroxygalactarate. This protein is known to increase colonization fitness of intestinal pathogens in antibiotic-treated mice and to promote bacterial survival during stress. The galactarate/glucarate pathway is widespread in bacteria, but not in humans, and thus could be a target to develop new inhibitors for use in combination therapy to combat antibiotic resistance. The structure of almost all the enzymes of the galactarate/glucarate pathway were solved previously, except for GarD, for which only the structure of the N-terminal domain was determined previously. Herein, we report the first crystal structure of full-length GarD solved using a seleno-methoionine derivative revealing a new protein fold. The protein consists of three domains, each presenting a novel twist as compared to their distant homologs. GarD in the crystal structure forms dimers and each monomer consists of three domains. The N-terminal domain is comprised of a β-clip fold, connected to the second domain by a long unstructured linker. The second domain serves as a dimerization interface between two monomers. The C-terminal domain forms an unusual variant of a Rossmann fold with a crossover and is built around a seven-stranded parallel β-sheet supported by nine α-helices. A metal binding site in the C-terminal domain is occupied by Ca 2+ . The activity of GarD was corroborated by the production of 5-keto-4-deoxy-D-glucarate under reducing conditions and in the presence of iron. Thus, GarD is an unusual enolase with a novel protein fold never previously seen in this class of enzymes.


  • Organizational Affiliation

    Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactarate dehydratase (L-threo-forming)
A, B
526Escherichia coli K-12Mutation(s): 0 
Gene Names: garDyhaGb3128JW3097
EC: 4.2.1.42
UniProt
Find proteins for P39829 (Escherichia coli (strain K12))
Explore P39829 
Go to UniProtKB:  P39829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39829
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Galactarate dehydratase (L-threo-forming)
C, D
526Escherichia coli K-12Mutation(s): 0 
Gene Names: garDyhaGb3128JW3097
EC: 4.2.1.42
UniProt
Find proteins for P39829 (Escherichia coli (strain K12))
Explore P39829 
Go to UniProtKB:  P39829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39829
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
L [auth B]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
K [auth A]
R [auth D]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
R [auth D],
S [auth D],
T [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
PHD
Query on PHD
A, B
L-PEPTIDE LINKINGC4 H8 N O7 PASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.462α = 90
b = 167.574β = 103.97
c = 117.065γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references, Derived calculations