PDBsum entry 2z6f

Heme binding protein

PDB id

2z6f

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Contents

			Protein chain

					112 a.a. *

			Ligands

					HEM

			Waters ×88

* Residue conservation analysis

PDB id:

2z6f

Links

Name:

Heme binding protein

Title:

Crystal structure of neat domain from staphylococcus aureus in complex with heme

Structure:

Iron-regulated surface determinant protein h. Chain: a. Fragment: neat 3 domain, residue 539-664. Synonym: haptoglobin receptor a, staphylococcus aureus surface protein i. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 158878. Strain: mu50. Gene: isdh. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.90Å

R-factor:

0.197

R-free:

0.242

Authors:

Y.Tanaka,A.Suenaga,K.Tsumoto

Key ref:

M.Watanabe et al. (2008). Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus. J Biol Chem, 283, 28649-28659. PubMed id: 18667422 DOI: 10.1074/jbc.M803383200

Date:

31-Jul-07

Release date:

29-Jul-08

PROCHECK

	Headers

	References

Protein chain

Q931P4 (ISDH_STAAM) - Iron-regulated surface determinant protein H from Staphylococcus aureus (strain Mu50 / ATCC 700699)

Seq: Struc:

Seq: Struc:					891 a.a. 112 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DOI no: 10.1074/jbc.M803383200	J Biol Chem 283:28649-28659 (2008)
PubMed id: 18667422

Structural basis for multimeric heme complexation through a specific protein-heme interaction: the case of the third neat domain of IsdH from Staphylococcus aureus.
M.Watanabe, Y.Tanaka, A.Suenaga, M.Kuroda, M.Yao, N.Watanabe, F.Arisaka, T.Ohta, I.Tanaka, K.Tsumoto.

ABSTRACT

To elucidate the heme acquisition system in pathogenic bacteria, we investigated the heme-binding properties of the third NEAT domain of IsdH (IsdH-NEAT3), a receptor for heme located on the surfaces of pathogenic bacterial cells, by using x-ray crystallography, isothermal titration calorimetry, examination of absorbance spectra, mutation analysis, size-exclusion chromatography, and analytical ultracentrifugation. We found the following: 1) IsdH-NEAT3 can bind with multiple heme molecules by two modes; 2) heme was bound at the surface of IsdH-NEAT3; 3) candidate residues proposed from the crystal structure were not essential for binding with heme; and 4) IsdH-NEAT3 was associated into a multimeric heme complex by the addition of excess heme. From these observations, we propose a heme-binding mechanism for IsdH-NEAT3 that involves multimerization and discuss the biological importance of this mechanism.

Selected figure(s)



	Figure 4. Comparison of residues around heme. A, IsdH-NEAT3. B, IsdA-NEAT (Protein Data Bank code 2ITF). C, IsdC-NEAT (Protein Data Bank code 2O6P). The bound heme molecules are shown as sticks, with pink carbons; the heme irons appear as orange balls. Residues coordinating heme iron and located around the heme are also shown as sticks; their carbons are shown as green.		Figure 8. Schematic representation of proposed mechanism of heme binding by IsdH-NEAT3. IsdH-NEAT3 and heme are shown as CPK space filling model and red stick model, respectively. The primary and secondary modes of heme binding described in the text are indicated.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21258843

E.S.Honsa, and A.W.Maresso (2011).
Mechanisms of iron import in anthrax.

Biometals, 24, 533-545.

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.

20147287

J.C.Grigg, J.D.Cooper, J.Cheung, D.E.Heinrichs, and M.E.Murphy (2010).
The Staphylococcus aureus siderophore receptor HtsA undergoes localized conformational changes to enclose staphyloferrin A in an arginine-rich binding pocket.

J Biol Chem, 285, 11162-11171.

PDB codes:

3lhs 3li2

20223800

M.Meehan, F.M.Burke, S.Macken, and P.Owen (2010).
Characterization of the haem-uptake system of the equine pathogen Streptococcus equi subsp. equi.

Microbiology, 156, 1824-1835.

20807204

M.Ouattara, E.B.Cunha, X.Li, Y.S.Huang, D.Dixon, and Z.Eichenbaum (2010).
Shr of group A streptococcus is a new type of composite NEAT protein involved in sequestering haem from methaemoglobin.

Mol Microbiol, 78, 739-756.

19917297

N.Chim, A.Iniguez, T.Q.Nguyen, and C.W.Goulding (2010).
Unusual diheme conformation of the heme-degrading protein from Mycobacterium tuberculosis.

J Mol Biol, 395, 595-608.

PDB code:

3hx9

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.

19759022

M.Fabian, E.Solomaha, J.S.Olson, and A.W.Maresso (2009).
Heme transfer to the bacterial cell envelope occurs via a secreted hemophore in the Gram-positive pathogen Bacillus anthracis.

J Biol Chem, 284, 32138-32146.

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 codes are shown on the right.