4AW7

BpGH86A: A beta-porphyranase of glycoside hydrolase family 86 from the human gut bacterium Bacteroides plebeius


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.137 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.

Hehemann, J.H.Kelly, A.G.Pudlo, N.A.Martens, E.C.Boraston, A.B.

(2012) Proc. Natl. Acad. Sci. U.S.A. 109: 19786-19791

  • DOI: 10.1073/pnas.1211002109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant ...

    Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are β-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 Å resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada V8W 3P6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GH86A BETA-PORPHYRANASE
A
591Bacteroides plebeius (strain DSM 17135 / JCM 12973 / M2)Mutation(s): 0 
EC: 3.2.1.178
Find proteins for B5CY96 (Bacteroides plebeius (strain DSM 17135 / JCM 12973 / M2))
Go to UniProtKB:  B5CY96
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
GAL
Query on GAL

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A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
EDO
Query on EDO

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A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
L6S
Query on L6S

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A
6-O-sulfo-alpha-L-galactose
C6 H12 O9 S
OKUVUONOJCDUJY-SXUWKVJYSA-N
 Ligand Interaction
AAL
Query on AAL

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Download CCD File 
A
3,6-ANHYDRO-L-GALACTOSE
C6 H10 O5
DCQFFOLNJVGHLW-DSOBHZJASA-N
 Ligand Interaction
GLA
Query on GLA

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A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.330α = 90.00
b = 87.700β = 90.00
c = 114.450γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-10-31
    Type: Atomic model, Other
  • Version 1.2: 2012-11-14
    Type: Database references, Other
  • Version 1.3: 2012-11-21
    Type: Database references
  • Version 1.4: 2012-12-26
    Type: Database references
  • Version 1.5: 2019-01-16
    Type: Data collection, Database references