6MGD

Thermosulfurimonas dismutans KpsC, beta Kdo 2,7 transferase

• PDB DOI:  https://doi.org/10.2210/pdb6MGD/pdb

• Classification: TRANSFERASE
• Organism(s): Thermosulfurimonas dismutans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-13 Released: 2019-03-27 
• Deposition Author(s): Doyle, L., Mallette, E., Kimber, M.S., Whitfield, C.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.260 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

Biosynthesis of a conserved glycolipid anchor for Gram-negative bacterial capsules.

Doyle, L., Ovchinnikova, O.G., Myler, K., Mallette, E., Huang, B.S., Lowary, T.L., Kimber, M.S., Whitfield, C.

(2019) Nat Chem Biol 15: 632-640

• PubMed: 31036922 
• DOI: https://doi.org/10.1038/s41589-019-0276-8
• Primary Citation of Related Structures:  
  6MGB, 6MGC, 6MGD


• PubMed Abstract: 
  

Several important Gram-negative bacterial pathogens possess surface capsular layers composed of hypervariable long-chain polysaccharides linked via a conserved 3-deoxy-β-D-manno-oct-2-ulosonic acid (β-Kdo) oligosaccharide to a phosphatidylglycerol residue. The pathway for synthesis of the terminal glycolipid was elucidated by determining the structures of reaction intermediates. In Escherichia coli, KpsS transfers a single Kdo residue to phosphatidylglycerol; this primer is extended using a single enzyme (KpsC), possessing two cytidine 5'-monophosphate (CMP)-Kdo-dependent glycosyltransferase catalytic centers with different linkage specificities. The structure of the N-terminal β-(2→4) Kdo transferase from KpsC reveals two α/β domains, supplemented by several helices. The N-terminal Rossmann-like domain, typically responsible for acceptor binding, is severely reduced in size compared with canonical GT-B folds in glycosyltransferases. The similar structure of the C-terminal β-(2→7) Kdo transferase indicates a past gene duplication event. Both Kdo transferases have a narrow active site tunnel, lined with key residues shared with GT99 β-Kdo transferases. This enzyme provides the prototype for the GT107 family.

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Organizational Affiliation: 

Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.57 kDa 
• Atom Count: 4,875 
• Modelled Residue Count: 589 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsular polysaccharide export system protein KpsC	A, B	332	Thermosulfurimonas dismutans	Mutation(s): 0  Gene Names: TDIS_1054
UniProt
Find proteins for A0A179D3Y0 (Thermosulfurimonas dismutans) Explore A0A179D3Y0  Go to UniProtKB:  A0A179D3Y0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.260 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.67	α = 90
b = 79.82	β = 109.12
c = 77.4	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Doyle, L., Mallette, E., Kimber, M.S., Whitfield, C.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	04045-2015
Canadian Institutes of Health Research (CIHR)	Canada	201509FDN-353054
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	--

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Database references
• Version 1.3: 2019-05-15
  Changes: Data collection, Database references
• Version 1.4: 2019-05-29
  Changes: Data collection, Database references
• Version 1.5: 2019-11-27
  Changes: Structure summary
• Version 1.6: 2020-01-08
  Changes: Author supporting evidence