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PDBsum entry 3ehm

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protein ligands links
Sugar binding protein PDB id
3ehm
Jmol
Contents
Protein chains
510 a.a. *
Ligands
EDO
Waters ×663
* Residue conservation analysis
PDB id:
3ehm
Name: Sugar binding protein
Title: Structure of bt1043
Structure: Susd homolog. Chain: a, b. Fragment: unp residues 18-546. Engineered: yes
Source: Bacteroides thetaiotaomicron. Organism_taxid: 818. Strain: vpi-5482. Gene: bt_1043. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.171     R-free:   0.207
Authors: N.M.Koropatkin,T.J.Smith
Key ref: N.Koropatkin et al. (2009). Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont. Biochemistry, 48, 1532-1542. PubMed id: 19191477
Date:
13-Sep-08     Release date:   12-May-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8A8X4  (Q8A8X4_BACTN) -  SusD homolog
Seq:
Struc:
 
Seq:
Struc:
546 a.a.
510 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 

 
Biochemistry 48:1532-1542 (2009)
PubMed id: 19191477  
 
 
Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.
N.Koropatkin, E.C.Martens, J.I.Gordon, T.J.Smith.
 
  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. 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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944222 C.Bakolitsa, Q.Xu, C.L.Rife, P.Abdubek, T.Astakhova, H.L.Axelrod, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1274-1280.
PDB code: 3cgh
20806225 T.K.Pham, S.Roy, J.Noirel, I.Douglas, P.C.Wright, and G.P.Stafford (2010).
A quantitative proteomic analysis of biofilm adaptation by the periodontal pathogen Tannerella forsythia.
  Proteomics, 10, 3130-3141.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.