6RB7 | pdb_00006rb7

Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.151 (Depositor), 0.163 (DCC) 
  • R-Value Work: 
    0.129 (Depositor), 0.143 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6RB7

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut.

Bell, A.Brunt, J.Crost, E.Vaux, L.Nepravishta, R.Owen, C.D.Latousakis, D.Xiao, A.Li, W.Chen, X.Walsh, M.A.Claesen, J.Angulo, J.Thomas, G.H.Juge, N.

(2019) Nat Microbiol 4: 2393-2404

  • DOI: https://doi.org/10.1038/s41564-019-0590-7
  • Primary Citation Related Structures: 
    6RAB, 6RB7, 6RD1

  • PubMed Abstract: 

    Sialic acid (N-acetylneuraminic acid (Neu5Ac)) is commonly found in the terminal location of colonic mucin glycans where it is a much-coveted nutrient for gut bacteria, including Ruminococcus gnavus. R. gnavus is part of the healthy gut microbiota in humans, but it is disproportionately represented in diseases. There is therefore a need to understand the molecular mechanisms that underpin the adaptation of R. gnavus to the gut. Previous in vitro research has demonstrated that the mucin-glycan-foraging strategy of R. gnavus is strain dependent and is associated with the expression of an intramolecular trans-sialidase, which releases 2,7-anhydro-Neu5Ac, rather than Neu5Ac, from mucins. Here, we unravelled the metabolism pathway of 2,7-anhydro-Neu5Ac in R. gnavus that is underpinned by the exquisite specificity of the sialic transporter for 2,7-anhydro-Neu5Ac and by the action of an oxidoreductase that converts 2,7-anhydro-Neu5Ac into Neu5Ac, which then becomes a substrate of a Neu5Ac-specific aldolase. Having generated an R. gnavus nan-cluster deletion mutant that lost the ability to grow on sialylated substrates, we showed that-in gnotobiotic mice colonized with R. gnavus wild-type (WT) and mutant strains-the fitness of the nan mutant was significantly impaired, with a reduced ability to colonize the mucus layer. Overall, we revealed a unique sialic acid pathway in bacteria that has important implications for the spatial adaptation of mucin-foraging gut symbionts in health and disease.


  • Organizational Affiliation
    • The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.

Macromolecule Content 

  • Total Structure Weight: 150.03 kDa 
  • Atom Count: 11,482 
  • Modeled Residue Count: 1,220 
  • Deposited Residue Count: 1,344 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative N-acetylneuraminate lyaseA,
B,
C [auth E],
D [auth F]
336Mediterraneibacter gnavus ATCC 29149Mutation(s): 0 
Gene Names: RUMGNA_02692
EC: 4.1.3.3
UniProt
Find proteins for A7B555 (Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9))
Explore A7B555 
Go to UniProtKB:  A7B555
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7B555
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCN

Query on BCN



Download:Ideal Coordinates CCD File
I [auth A]BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B],
O [auth E],
R [auth F]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A],
T [auth F],
U [auth F]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
H [auth A]
J [auth A]
M [auth B]
P [auth E]
F [auth A],
H [auth A],
J [auth A],
M [auth B],
P [auth E],
S [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
K [auth A],
N [auth B],
Q [auth E],
V [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.151 (Depositor), 0.163 (DCC) 
  • R-Value Work:  0.129 (Depositor), 0.143 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.181α = 90
b = 121.39β = 109.49
c = 86.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
MrBUMPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M011216/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description