5G2T

BT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4 D-Glucosamine-2-N, 6-O-disulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans.

Cartmell, A.Lowe, E.C.Basle, A.Firbank, S.J.Ndeh, D.A.Murray, H.Terrapon, N.Lombard, V.Henrissat, B.Turnbull, J.E.Czjzek, M.Gilbert, H.J.Bolam, D.N.

(2017) Proc Natl Acad Sci U S A 114: 7037-7042

  • DOI: https://doi.org/10.1073/pnas.1704367114
  • Primary Citation of Related Structures:  
    4AK1, 4AK2, 5G2T, 5G2U, 5G2V

  • PubMed Abstract: 

    The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron , a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides , indicating that the model developed is of generic relevance to this important microbial community.


  • Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-O GLYCOSAMINOGLYCAN SULFATASE
A, B, C, D
489Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
EC: 3.1.6.18 (PDB Primary Data), 3.1.6 (UniProt)
UniProt
Find proteins for Q8A7C8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A7C8 
Go to UniProtKB:  Q8A7C8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A7C8
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
E, F
2N/AN/A
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UAP
Query on UAP

Download Ideal Coordinates CCD File 
LA [auth C],
WA [auth D]
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid
C6 H8 O9 S
VJIMUKBSNUBECH-YKKSOZKNSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth C],
G [auth A],
NA [auth D],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
GA [auth C]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth D],
PA [auth D],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
SA [auth D],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B],
MA [auth C],
P [auth A],
VA [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.207α = 90
b = 114.526β = 100.04
c = 127.293γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-05-31
    Changes: Structure summary
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model
  • Version 2.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary