Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.34 kDa 
• Atom Count: 3310 
• Modelled Residue Count: 309 
• Deposited Residue Count: 312 
• Unique protein chains: 1

2XWV

SiaP complex

• DOI: 10.2210/pdb2XWV/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Haemophilus influenzae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-05 Released: 2011-11-16 
• Deposition Author(s): Fischer, M., Hubbard, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.150 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 

Literature

Tripartite ATP-Independent Periplasmic (Trap) Transporters Use an Arginine-Mediated Selectivity Filter for High Affinity Substrate Binding.

Fischer, M., Hopkins, A.P., Severi, E., Hawkhead, J., Bawdon, D., Watts, A.G., Hubbard, R.E., Thomas, G.H.

(2015) J Biol Chem 290: 27113

• PubMed: 26342690 
• DOI: 10.1074/jbc.M115.656603
• Primary Citation of Related Structures:  
  2XWV, 2XWI, 2XWK, 2XWO


• PubMed Abstract: 
  

Tripartite ATP-independent periplasmic (TRAP) transporters are secondary transporters that have evolved an obligate dependence on a substrate-binding protein (SBP) to confer unidirectional transport. Different members of the DctP family of TRAP SBPs have binding sites that recognize a diverse range of organic acid ligands but appear to only share a common electrostatic interaction between a conserved arginine and a carboxylate group in the ligand. We investigated the significance of this interaction using the sialic acid-specific SBP, SiaP, from the Haemophilus influenzae virulence-related SiaPQM TRAP transporter. Using in vitro, in vivo, and structural methods applied to SiaP, we demonstrate that the coordination of the acidic ligand moiety of sialic acid by the conserved arginine (Arg-147) is essential for the function of the transporter as a high affinity scavenging system. However, at high substrate concentrations, the transporter can function in the absence of Arg-147 suggesting that this bi-molecular interaction is not involved in further stages of the transport cycle. As well as being required for high affinity binding, we also demonstrate that the Arg-147 is a strong selectivity filter for carboxylate-containing substrates in TRAP transporters by engineering the SBP to recognize a non-carboxylate-containing substrate, sialylamide, through water-mediated interactions. Together, these data provide biochemical and structural support that TRAP transporters function predominantly as high affinity transporters for carboxylate-containing substrates.

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Organizational Affiliation: 

Biology (Area 10), University of York, P. O. Box 373, York YO10 5YW and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP	A	312	Haemophilus influenzae	Mutation(s): 0
Find proteins for P44542 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44542  Go to UniProtKB:  P44542

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLB	B [auth A]	N-acetyl-beta-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-PFQGKNLYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.150 
• R-Value Work: 0.125 
• R-Value Observed: 0.126 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.723	α = 90
b = 74.51	β = 90
c = 86.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
ACORN	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-05 
• Released Date: 2011-11-16 
Deposition Author(s): Fischer, M., Hubbard, R.E.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2011-11-23
  Changes: Structure summary
• Version 1.2: 2015-09-16
  Changes: Database references
• Version 1.3: 2015-09-23
  Changes: Database references
• Version 1.4: 2015-11-18
  Changes: Database references
• Version 1.5: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.6: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary