5MWK

Glycoside hydrolase BT_0986


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Complex pectin metabolism by gut bacteria reveals novel catalytic functions.

Ndeh, D.Rogowski, A.Cartmell, A.Luis, A.S.Basle, A.Gray, J.Venditto, I.Briggs, J.Zhang, X.Labourel, A.Terrapon, N.Buffetto, F.Nepogodiev, S.Xiao, Y.Field, R.A.Zhu, Y.O'Neill, M.A.Urbanowicz, B.R.York, W.S.Davies, G.J.Abbott, D.W.Ralet, M.C.Martens, E.C.Henrissat, B.Gilbert, H.J.

(2017) Nature 544: 65-70

  • DOI: 10.1038/nature21725
  • Primary Citation of Related Structures:  5MQM, 5MQN, 5MQO, 5MQR, 5MQS, 5MSX, 5MSY, 5MT2, 5MUI, 5MUJ

  • PubMed Abstract: 
  • The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bac ...

    The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase family 2, sugar binding protein
A
1105Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)N/A
Find proteins for Q8A931 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Go to UniProtKB:  Q8A931
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARA
Query on ARA

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A
ALPHA-L-ARABINOSE
C5 H10 O5
SRBFZHDQGSBBOR-QMKXCQHVSA-N
 Ligand Interaction
IOD
Query on IOD

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

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A
ALPHA-L-RHAMNOSE
C6 H12 O5
SHZGCJCMOBCMKK-HGVZOGFYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

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A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
8OQ
Query on 8OQ

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A
alpha-D-aceric acid
C6 H10 O6
PAIOZXJXGSOKFN-SYXVZTBSSA-N
 Ligand Interaction
GAL
Query on GAL

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A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
8PK
Query on 8PK

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A
2-O-methyl, 4-O-Acetyl-alpha-L-fucosepyranose
C9 H18 O6
MOOIWRPNHMPYOB-BARZSYDPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.254α = 90.00
b = 86.216β = 99.38
c = 123.200γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references
  • Version 1.2: 2017-04-12
    Type: Database references