6PTM

Crystal structure of apo exo-carrageenase GH42 from Bacteroides ovatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.

Hettle, A.G.Hobbs, J.K.Pluvinage, B.Vickers, C.Abe, K.T.Salama-Alber, O.McGuire, B.E.Hehemann, J.H.Hui, J.P.M.Berrue, F.Banskota, A.Zhang, J.Bottos, E.M.Van Hamme, J.Boraston, A.B.

(2019) Commun Biol 2: 474-474

  • DOI: 10.1038/s42003-019-0721-y
  • Primary Citation of Related Structures:  
    6PNU, 6POP, 6PRM, 6PSM, 6PSO, 6PT4, 6PT6, 6PT9, 6PTK, 6PTM

  • PubMed Abstract: 
  • Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides ...

    Pseudoalteromonas is a globally distributed marine-associated genus that can be found in a broad range of aquatic environments, including in association with macroalgal surfaces where they may take advantage of these rich sources of polysaccharides. The metabolic systems that confer the ability to metabolize this abundant form of photosynthetically fixed carbon, however, are not yet fully understood. Through genomics, transcriptomics, microbiology, and specific structure-function studies of pathway components we address the capacity of newly isolated marine pseudoalteromonads to metabolize the red algal galactan carrageenan. The results reveal that the κ/ι-carrageenan specific polysaccharide utilization locus (CarPUL) enables isolates possessing this locus the ability to grow on this substrate. Biochemical and structural analysis of the enzymatic components of the CarPUL promoted the development of a detailed model of the κ/ι-carrageenan metabolic pathway deployed by pseudoalteromonads, thus furthering our understanding of how these microbes have adapted to a unique environmental niche.


    Organizational Affiliation

    1Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA773Bacteroides ovatus CL02T12C04Mutation(s): 0 
Gene Names: HMPREF1069_02044
UniProt
Find proteins for I8YN04 (Bacteroides ovatus CL02T12C04)
Explore I8YN04 
Go to UniProtKB:  I8YN04
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.24α = 90
b = 109.69β = 90
c = 126.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-15
    Changes: Database references