PDBsum entry 2bkm

Oxygen storage

PDB id

2bkm

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Contents

			Protein chains

					128 a.a. *

			Ligands

					OXY-HEM-ACT ×2

			Waters ×347

* Residue conservation analysis

PDB id:

2bkm

Links

Name:

Oxygen storage

Title:

Crystal structure of the truncated hemoglobin from geobacillus stearothermophilus

Structure:

Truncated hemoglobin from geobacillus stearothermophilus. Chain: a, b. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: tuner.

Resolution:

1.50Å

R-factor:

0.168

R-free:

0.194

Authors:

A.Ilari,P.Kjelgaard,C.Von Wachenfeldt,A.Boffi,E.Chiancone

Key ref:

A.Ilari et al. (2007). Crystal structure and ligand binding properties of the truncated hemoglobin from Geobacillus stearothermophilus. Arch Biochem Biophys, 457, 85-94. PubMed id: 17126283

Date:

08-Feb-06

Release date:

29-Nov-06

PROCHECK

	Headers

	References

Protein chains

Q5L1S0 (Q5L1S0_GEOKA) - Hypothetical conserved protein from Geobacillus kaustophilus (strain HTA426)

Seq: Struc:					137 a.a. 128 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

	Arch Biochem Biophys 457:85-94 (2007)
PubMed id: 17126283

Crystal structure and ligand binding properties of the truncated hemoglobin from Geobacillus stearothermophilus.
A.Ilari, P.Kjelgaard, C.von Wachenfeldt, B.Catacchio, E.Chiancone, A.Boffi.

ABSTRACT

A novel truncated hemoglobin has been identified in the thermophilic bacterium Geobacillus stearothermophilus (Gs-trHb). The protein has been expressed in Escherichia coli, the 3D crystal structure (at 1.5 Angstroms resolution) and the ligand binding properties have been determined. The distal heme pocket displays an array of hydrogen bonding donors to the iron-bound ligands, including Tyr-B10 on one side of the heme pocket and Trp-G8 indole nitrogen on the opposite side. At variance with the highly similar Bacillus subtilis hemoglobin, Gs-trHb is dimeric both in the crystal and in solution and displays several unique structural properties. In the crystal cell, the iron-bound ligand is not homogeneously distributed within each distal site such that oxygen and an acetate anion can be resolved with relative occupancies of 50% each. Accordingly, equilibrium titrations of the oxygenated derivative in solution with acetate anion yield a partially saturated ferric acetate adduct. Moreover, the asymmetric unit contains two subunits and sedimentation velocity ultracentrifugation data confirm that the protein is dimeric.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21298303

J.Igarashi, K.Kobayashi, and A.Matsuoka (2011).
A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification.

J Biol Inorg Chem, 16, 599-609.

PDB codes:

3aq5 3aq6 3aq7 3aq8 3aq9

21445853

M.S.Heroux, A.D.Mohan, and K.W.Olsen (2011).
Ligand migration in the truncated hemoglobin of Mycobacterium tuberculosis.

IUBMB Life, 63, 214-220.

18548291

G.Razzera, J.Vernal, D.Baruh, V.I.Serpa, C.Tavares, F.Lara, E.M.Souza, F.O.Pedrosa, F.C.Almeida, H.Terenzi, and A.P.Valente (2008).
Spectroscopic characterization of a truncated hemoglobin from the nitrogen-fixing bacterium Herbaspirillum seropedicae.

J Biol Inorg Chem, 13, 1085-1096.

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.