5WH8

Cellulase Cel5C_n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.

Naas, A.E.Solden, L.M.Norbeck, A.D.Brewer, H.Hagen, L.H.Heggenes, I.M.McHardy, A.C.Mackie, R.I.Pasa-Tolic, L.Arntzen, M.O.Eijsink, V.G.H.Koropatkin, N.M.Hess, M.Wrighton, K.C.Pope, P.B.

(2018) Microbiome 6: 44-44

  • DOI: https://doi.org/10.1186/s40168-018-0421-8
  • Primary Citation of Related Structures:  
    5WH8

  • PubMed Abstract: 

    In nature, obligate herbivorous ruminants have a close symbiotic relationship with their gastrointestinal microbiome, which proficiently deconstructs plant biomass. Despite decades of research, lignocellulose degradation in the rumen has thus far been attributed to a limited number of culturable microorganisms. Here, we combine meta-omics and enzymology to identify and describe a novel Bacteroidetes family ("Candidatus MH11") composed entirely of uncultivated strains that are predominant in ruminants and only distantly related to previously characterized taxa. The first metabolic reconstruction of Ca. MH11-affiliated genome bins, with a particular focus on the provisionally named "Candidatus Paraporphyromonas polyenzymogenes", illustrated their capacity to degrade various lignocellulosic substrates via comprehensive inventories of singular and multi-modular carbohydrate active enzymes (CAZymes). Closer examination revealed an absence of archetypical polysaccharide utilization loci found in human gut microbiota. Instead, we identified many multi-modular CAZymes putatively secreted via the Bacteroidetes-specific type IX secretion system (T9SS). This included cellulases with two or more catalytic domains, which are modular arrangements that are unique to Bacteroidetes species studied to date. Core metabolic proteins from Ca. P. polyenzymogenes were detected in metaproteomic data and were enriched in rumen-incubated plant biomass, indicating that active saccharification and fermentation of complex carbohydrates could be assigned to members of this novel family. Biochemical analysis of selected Ca. P. polyenzymogenes CAZymes further iterated the cellulolytic activity of this hitherto uncultured bacterium towards linear polymers, such as amorphous and crystalline cellulose as well as mixed linkage β-glucans. We propose that Ca. P. polyenzymogene genotypes and other Ca. MH11 members actively degrade plant biomass in the rumen of cows, sheep and most likely other ruminants, utilizing singular and multi-domain catalytic CAZymes secreted through the T9SS. The discovery of a prominent role of multi-modular cellulases in the Gram-negative Bacteroidetes, together with similar findings for Gram-positive cellulosomal bacteria (Ruminococcus flavefaciens) and anaerobic fungi (Orpinomyces sp.), suggests that complex enzymes are essential and have evolved within all major cellulolytic dominions inherent to the rumen.


  • Organizational Affiliation

    Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Post Office Box 5003, 1432, Ås, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative carbohydrate-active enzyme323uncultured organismMutation(s): 0 
Gene Names: SARM_0026
UniProt
Find proteins for E9NSK2 (uncultured organism)
Explore E9NSK2 
Go to UniProtKB:  E9NSK2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9NSK2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
O [auth A],
P [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
Q [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.21α = 90
b = 75.5β = 90
c = 88.83γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of NorwayNorway214042
European Research Commission Starting Grant FellowshipNorway336355 - MicroDE

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary