PDBsum entry 2cey

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protein metals links
Transport PDB id
Protein chain
306 a.a. *
_ZN ×3
Waters ×295
* Residue conservation analysis
PDB id:
Name: Transport
Title: Apo structure of siap
Structure: Protein hi0146. Chain: a. Synonym: siap. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 727. Expressed in: escherichia coli. Expression_system_taxid: 469008.
1.70Å     R-factor:   0.196     R-free:   0.236
Authors: A.Muller,E.Severi,C.Mulligan,A.G.Watts,D.J.Kelly,K.S.Wilson, A.J.Wilkinson,G.H.Thomas
Key ref:
A.Müller et al. (2006). Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae. J Biol Chem, 281, 22212-22222. PubMed id: 16702222 DOI: 10.1074/jbc.M603463200
11-Feb-06     Release date:   15-May-06    
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Protein chain
Pfam   ArchSchema ?
P44542  (SIAP_HAEIN) -  Sialic acid-binding periplasmic protein SiaP
329 a.a.
306 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     transport   2 terms 


DOI no: 10.1074/jbc.M603463200 J Biol Chem 281:22212-22222 (2006)
PubMed id: 16702222  
Conservation of structure and mechanism in primary and secondary transporters exemplified by SiaP, a sialic acid binding virulence factor from Haemophilus influenzae.
A.Müller, E.Severi, C.Mulligan, A.G.Watts, D.J.Kelly, K.S.Wilson, A.J.Wilkinson, G.H.Thomas.
Extracytoplasmic solute receptors (ESRs) are important components of solute uptake systems in bacteria, having been studied extensively as parts of ATP binding cassette transporters. Herein we report the first crystal structure of an ESR protein from a functionally characterized electrochemical ion gradient dependent secondary transporter. This protein, SiaP, forms part of a tripartite ATP-independent periplasmic transporter specific for sialic acid in Haemophilus influenzae. Surprisingly, the structure reveals an overall topology similar to ATP binding cassette ESR proteins, which is not apparent from the sequence, demonstrating that primary and secondary transporters can share a common structural component. The structure of SiaP in the presence of the sialic acid analogue 2,3-didehydro-2-deoxy-N-acetylneuraminic acid reveals the ligand bound in a deep cavity with its carboxylate group forming a salt bridge with a highly conserved Arg residue. Sialic acid binding, which obeys simple bimolecular association kinetics as determined by stopped-flow fluorescence spectroscopy, is accompanied by domain closure about a hinge region and the kinking of an alpha-helix hinge component. The structure provides insight into the evolution, mechanism, and substrate specificity of ESR-dependent secondary transporters that are widespread in prokaryotes.
  Selected figure(s)  
Figure 1.
FIGURE 1. Overall structure of the unliganded (A) and Neu5Ac2en-bound (B) forms of SiaP and the superposition by least squares minimization procedures applied to the positions of the C atoms of domain I (C) in an orientation to illustrate the domain closure around the ligand. The ribbon diagrams were drawn using CCP4MG (52), and the ligand is colored by atom type. D, surface representation of the Neu5Ac2en structure viewed looking down into the binding cleft. The ligand is in blue, and domain I is on the left, whereas domain II is on the right.
Figure 5.
FIGURE 5. Chemical structures and K[d] values of sialic acid (Neu5Ac) and related analogues used in this study and in Severi et al. (13). Neu5Gc, N-glycolylneuraminic acid; KDN, 2-keto-3-deoxy-D-glycero-D-galactonononic acid.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 22212-22222) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20584082 C.Mulligan, M.Fischer, and G.H.Thomas (2011).
Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea.
  FEMS Microbiol Rev, 35, 68-86.  
20100283 E.Severi, A.H.Hosie, J.A.Hawkhead, and G.H.Thomas (2010).
Characterization of a novel sialic acid transporter of the sodium solute symporter (SSS) family and in vivo comparison with known bacterial sialic acid transporters.
  FEMS Microbiol Lett, 304, 47-54.  
20656493 M.Fischer, Q.Y.Zhang, R.E.Hubbard, and G.H.Thomas (2010).
Caught in a TRAP: substrate-binding proteins in secondary transport.
  Trends Microbiol, 18, 471-478.  
19179287 C.Mulligan, E.R.Geertsma, E.Severi, D.J.Kelly, B.Poolman, and G.H.Thomas (2009).
The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter.
  Proc Natl Acad Sci U S A, 106, 1778-1783.  
19744923 R.S.Horler, A.Müller, D.C.Williamson, J.R.Potts, K.S.Wilson, and G.H.Thomas (2009).
Furanose-specific sugar transport: characterization of a bacterial galactofuranose-binding protein.
  J Biol Chem, 284, 31156-31163.
PDB code: 2vk2
18723845 M.J.Cuneo, A.Changela, A.E.Miklos, L.S.Beese, J.K.Krueger, and H.W.Hellinga (2008).
Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport.
  J Biol Chem, 283, 32812-32820.
PDB code: 2hpg
19019243 M.J.Cuneo, L.S.Beese, and H.W.Hellinga (2008).
Ligand-induced conformational changes in a thermophilic ribose-binding protein.
  BMC Struct Biol, 8, 50.
PDB codes: 2fn8 2fn9
17362499 S.Gonin, P.Arnoux, B.Pierru, J.Lavergne, B.Alonso, M.Sabaty, and D.Pignol (2007).
Crystal structures of an Extracytoplasmic Solute Receptor from a TRAP transporter in its open and closed forms reveal a helix-swapped dimer requiring a cation for alpha-keto acid binding.
  BMC Struct Biol, 7, 11.
PDB codes: 2hzk 2hzl
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