PDBsum entry 2rg7

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protein Protein-protein interface(s) links
Transport protein PDB id
Protein chains
255 a.a. *
Waters ×246
* Residue conservation analysis
PDB id:
Name: Transport protein
Title: Apo- crystal structure of a periplasmic heme binding protein from shigella dysenteriae
Structure: Periplasmic heme binding protein. Chain: a, b, c, d. Engineered: yes
Source: Shigella dysenteriae. Organism_taxid: 622. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.05Å     R-factor:   0.232     R-free:   0.274
Authors: W.W.Ho,H.Li
Key ref:
W.W.Ho et al. (2007). Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins. J Biol Chem, 282, 35796-35802. PubMed id: 17925389 DOI: 10.1074/jbc.M706761200
02-Oct-07     Release date:   09-Oct-07    
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Protein chains
Pfam   ArchSchema ?
O70018  (O70018_SHIDY) -  Putative uncharacterized protein shuT
304 a.a.
255 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M706761200 J Biol Chem 282:35796-35802 (2007)
PubMed id: 17925389  
Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins.
W.W.Ho, H.Li, S.Eakanunkul, Y.Tong, A.Wilks, M.Guo, T.L.Poulos.
An essential component of heme transport in Gram-negative bacterial pathogens is the periplasmic protein that shuttles heme between outer and inner membranes. We have solved the first crystal structures of two such proteins, ShuT from Shigella dysenteriae and PhuT from Pseudomonas aeruginosa. Both share a common architecture typical of Class III periplasmic binding proteins. The heme binds in a narrow cleft between the N- and C-terminal binding domains and is coordinated by a Tyr residue. A comparison of the heme-free (apo) and -bound (holo) structures indicates little change in structure other than minor alterations in the heme pocket and movement of the Tyr heme ligand from an "in" position where it can coordinate the heme iron to an "out" orientation where it points away from the heme pocket. The detailed architecture of the heme pocket is quite different in ShuT and PhuT. Although Arg(228) in PhuT H-bonds with a heme propionate, in ShuT a peptide loop partially takes up the space occupied by Arg(228), and there is no Lys or Arg H-bonding with the heme propionates. A comparison of PhuT/ShuT with the vitamin B(12)-binding protein BtuF and the hydroxamic-type siderophore-binding protein FhuD, the only two other structurally characterized Class III periplasmic binding proteins, demonstrates that PhuT/ShuT more closely resembles BtuF, which reflects the closer similarity in ligands, heme and B(12), compared with ligands for FhuD, a peptide siderophore.
  Selected figure(s)  
Figure 2.
FIGURE 2. Heme binding pocket in PhuT and ShuT. The maps shown are 2F[o] - F[c] maps contoured at 1.0 . A, in PhuT Arg^228 H-bonds with one heme propionate, whereas Arg^73 in the proximal pocket is close enough for H-bonding interactions with the Tyr^71 ligand. B, the partially bound heme in ShuT structure has Lys^69 nearby. To form an H-bond with the Tyr ligand an unfavorable bending of the side chain would be required.
Figure 3.
FIGURE 3. Comparison of the Tyr ligand in and out conformations in ShuT. Tyr^67 in the in conformation is shown in blue, and the out conformation is shown in magenta.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 35796-35802) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21194366 B.C.Chu, and H.J.Vogel (2011).
A structural and functional analysis of type III periplasmic and substrate binding proteins: their role in bacterial siderophore and heme transport.
  Biol Chem, 392, 39-52.  
21339081 J.A.Mayfield, C.A.Dehner, and J.L.DuBois (2011).
Recent advances in bacterial heme protein biochemistry.
  Curr Opin Chem Biol, 15, 260-266.  
21383189 M.V.Tullius, C.A.Harmston, C.P.Owens, N.Chim, R.P.Morse, L.M.McMath, A.Iniguez, J.M.Kimmey, M.R.Sawaya, J.P.Whitelegge, M.A.Horwitz, and C.W.Goulding (2011).
Discovery and characterization of a unique mycobacterial heme acquisition system.
  Proc Natl Acad Sci U S A, 108, 5051-5056.
PDB code: 3may
20497229 T.Eitinger, D.A.Rodionov, M.Grote, and E.Schneider (2011).
Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions.
  FEMS Microbiol Rev, 35, 3.  
20810662 J.C.Grigg, J.Cheung, D.E.Heinrichs, and M.E.Murphy (2010).
Specificity of Staphyloferrin B recognition by the SirA receptor from Staphylococcus aureus.
  J Biol Chem, 285, 34579-34588.  
20173761 O.Lewinson, A.T.Lee, K.P.Locher, and D.C.Rees (2010).
A distinct mechanism for the ABC transporter BtuCD-BtuF revealed by the dynamics of complex formation.
  Nat Struct Mol Biol, 17, 332-338.  
20352420 P.Cornelis (2010).
Iron uptake and metabolism in pseudomonads.
  Appl Microbiol Biotechnol, 86, 1637-1645.  
19703464 A.E.Medlock, M.Carter, T.A.Dailey, H.A.Dailey, and W.N.Lanzilotta (2009).
Product release rather than chelation determines metal specificity for ferrochelatase.
  J Mol Biol, 393, 308-319.
PDB codes: 3hcn 3hco 3hcp 3hcr
19955416 A.M.Zawadzka, Y.Kim, N.Maltseva, R.Nichiporuk, Y.Fan, A.Joachimiak, and K.N.Raymond (2009).
Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore.
  Proc Natl Acad Sci U S A, 106, 21854-21859.
PDB code: 3gfv
19420687 F.Andreoni, R.Boiani, G.Serafini, I.Bianconi, S.Dominici, F.Gorini, and M.Magnani (2009).
Expression, purification, and characterization of the recombinant putative periplasmic hemin-binding protein (HutB) of Photobacterium damselae subsp. piscicida.
  Biosci Biotechnol Biochem, 73, 1180-1183.  
19400778 F.C.Beasley, E.D.Vinés, J.C.Grigg, Q.Zheng, S.Liu, G.A.Lajoie, M.E.Murphy, and D.E.Heinrichs (2009).
Characterization of staphyloferrin A biosynthetic and transport mutants in Staphylococcus aureus.
  Mol Microbiol, 72, 947-963.
PDB codes: 3eiw 3eix
18977196 Y.Tong, and M.Guo (2009).
Bacterial heme-transport proteins and their heme-coordination modes.
  Arch Biochem Biophys, 481, 1.  
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.