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PDBsum entry 3ck9

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protein ligands metals Protein-protein interface(s) links
Sugar binding protein PDB id
3ck9
Jmol
Contents
Protein chains
508 a.a. *
Ligands
EDO ×13
GLC-GLC-GLC-GLC-
GLC-GLC-GLC
GLC-GLC-GLC-GLC-
GLC-GLC
Metals
_CA ×4
Waters ×728
* Residue conservation analysis
PDB id:
3ck9
Name: Sugar binding protein
Title: B. Thetaiotaomicron susd with maltoheptaose
Structure: Susd. Chain: a, b. Fragment: unp residues 26-551. Engineered: yes
Source: Bacteroides thetaiotaomicron. Strain: vpi-5482. Gene: susd. Expressed in: escherichia coli.
Resolution:
2.20Å     R-factor:   0.185     R-free:   0.222
Authors: N.M.Koropatkin,E.C.Martens,J.I.Gordon,T.J.Smith
Key ref:
N.M.Koropatkin et al. (2008). Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure, 16, 1105-1115. PubMed id: 18611383 DOI: 10.1016/j.str.2008.03.017
Date:
14-Mar-08     Release date:   20-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8A1G2  (Q8A1G2_BACTN) -  Starch-binding protein SusD
Seq:
Struc:
 
Seq:
Struc:
551 a.a.
508 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     carbohydrate metabolic process   3 terms 
  Biochemical function     starch binding     3 terms  

 

 
DOI no: 10.1016/j.str.2008.03.017 Structure 16:1105-1115 (2008)
PubMed id: 18611383  
 
 
Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.
N.M.Koropatkin, E.C.Martens, J.I.Gordon, T.J.Smith.
 
  ABSTRACT  
 
The human gut microbiota performs functions that are not encoded in our Homo sapiens genome, including the processing of otherwise undigestible dietary polysaccharides. Defining the structures of proteins involved in the import and degradation of specific glycans by saccharolytic bacteria complements genomic analysis of the nutrient-processing capabilities of gut communities. Here, we describe the atomic structure of one such protein, SusD, required for starch binding and utilization by Bacteroides thetaiotaomicron, a prominent adaptive forager of glycans in the distal human gut microbiota. The binding pocket of this unique alpha-helical protein contains an arc of aromatic residues that complements the natural helical structure of starch and imposes this conformation on bound maltoheptaose. Furthermore, SusD binds cyclic oligosaccharides with higher affinity than linear forms. The structures of several SusD/oligosaccharide complexes reveal an inherent ligand recognition plasticity dominated by the three-dimensional conformation of the oligosaccharides rather than specific interactions with the composite sugars.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. SusD Complexed with Maltoheptaose
(A) The electron density of bound maltoheptaose from the corresponding omit map contoured at 3σ is shown.
(B) Important hydrophobic-stacking and hydrogen-bonding interactions between the maltoheptaose and SusD are detailed.
(C) Stereo diagram of SusD in the presence (blue) and absence (mauve) of bound maltoheptaose to highlight the conformational changes that occur upon oligosaccharide binding.
Figure 6.
Figure 6. SusD Complexed with α-Cyclodextrin
(A) Ribbon and surface rendering of α-cyclodextrin complexed with two copies of SusD.
(B) Omit map contoured at 3σ for bound α-cyclodextrin.
(C) Important ring-stacking and hydrogen-bonding interactions (distances in Å) are shown for the α-cyclodextrin/SusD complex.
 
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1105-1115) copyright 2008.  
  Figures were selected by the author.  

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
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae.
  Mol Microbiol, 77, 183-199.
PDB codes: 2xd2 2xd3
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
20668243 P.B.Pope, S.E.Denman, M.Jones, S.G.Tringe, K.Barry, S.A.Malfatti, A.C.McHardy, J.F.Cheng, P.Hugenholtz, C.S.McSweeney, and M.Morrison (2010).
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.
  Proc Natl Acad Sci U S A, 107, 14793-14798.  
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
19553672 E.C.Martens, N.M.Koropatkin, T.J.Smith, and J.I.Gordon (2009).
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm.
  J Biol Chem, 284, 24673-24677.  
19403529 E.C.Martens, R.Roth, J.E.Heuser, and J.I.Gordon (2009).
Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent human gut symbiont.
  J Biol Chem, 284, 18445-18457.  
19684063 J.P.Lewis, D.Iyer, and C.Anaya-Bergman (2009).
Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate.
  Microbiology, 155, 3758-3774.  
19321416 M.A.Mahowald, F.E.Rey, H.Seedorf, P.J.Turnbaugh, R.S.Fulton, A.Wollam, N.Shah, C.Wang, V.Magrini, R.K.Wilson, B.L.Cantarel, P.M.Coutinho, B.Henrissat, L.W.Crock, A.Russell, N.C.Verberkmoes, R.L.Hettich, and J.I.Gordon (2009).
Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla.
  Proc Natl Acad Sci U S A, 106, 5859-5864.  
19717629 M.J.McBride, G.Xie, E.C.Martens, A.Lapidus, B.Henrissat, R.G.Rhodes, E.Goltsman, W.Wang, J.Xu, D.W.Hunnicutt, A.M.Staroscik, T.R.Hoover, Y.Q.Cheng, and J.L.Stein (2009).
Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis.
  Appl Environ Microbiol, 75, 6864-6875.  
19191477 N.Koropatkin, E.C.Martens, J.I.Gordon, and T.J.Smith (2009).
Structure of a SusD homologue, BT1043, involved in mucin O-glycan utilization in a prominent human gut symbiont.
  Biochemistry, 48, 1532-1542.
PDB codes: 3ehm 3ehn
18611370 H.J.Gilbert (2008).
Sus out sugars in.
  Structure, 16, 987-989.  
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.