3EHN

BT1043 with N-acetyllactosamine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 

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This is version 2.0 of the entry. See complete history. 


Literature

Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.

Koropatkin, N., Martens, E.C., Gordon, J.I., Smith, T.J.

(2009) Biochemistry 48: 1532-1542

  • DOI: 10.1021/bi801942a
  • Primary Citation of Related Structures:  
    3EHM, 3EHN

  • PubMed Abstract: 

    • Mammalian distal gut bacteria have an expanded capacity to utilize glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth ...

    Mammalian distal gut bacteria have an expanded capacity to utilize glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth. The molecular basis of host glycan recognition by this species is still unknown but likely occurs through an expanded suite of outermembrane glycan-binding proteins that are the primary interface between B. thetaiotaomicron and its environment. Presented here is the atomic structure of the B. thetaiotaomicron protein BT1043, an outer membrane lipoprotein involved in host glycan metabolism. Despite a lack of detectable amino acid sequence similarity, BT1043 is a structural homologue of the B. thetaiotaomicron starch-binding protein SusD. Both structures are dominated by tetratrico peptide repeats that may facilitate association with outer membrane beta-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine reveals that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide. This is in contrast to CBM 32 family members that target the terminal nonreducing galactose residue of mucin glycans. The highly articulated glycan-binding pocket of BT1043 suggests that binding of ligands to BT1043 relies more upon interactions with the composite sugar residues than upon overall ligand conformation as previously observed for SusD. The diversity in amino acid sequence level likely reflects early divergence from a common ancestor, while the unique and conserved alpha-helical fold the SusD family suggests a similar function in glycan uptake.

    Organizational Affiliation: 

    Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SusD homologA, B532Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: BT1043, BT_1043
UniProt
Find proteins for Q8A8X4 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A8X4 
Go to UniProtKB:  Q8A8X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A8X4
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranoseC, D 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G79333MY
GlyCosmos:  G79333MY
GlyGen:  G79333MY
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.196 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.09α = 90
b = 156.09β = 90
c = 156.09γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary