Crystallographic Structure of Mycobacterium tuberculosis Hemoglobin O

Experimental Data Snapshot

  • Resolution: 2.11 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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A TyrCD1/TrpG8 hydrogen bond network and a TyrB10-TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O

Milani, M.Savard, P.-Y.Oullet, H.Ascenzi, P.Guertin, M.Bolognesi, M.

(2003) Proc Natl Acad Sci U S A 100: 5766-5771

  • DOI: https://doi.org/10.1073/pnas.1037676100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Truncated hemoglobins (Hbs) are small hemoproteins, identified in microorganisms and in some plants, forming a separate cluster within the Hb superfamily. Two distantly related truncated Hbs, trHbN and trHbO, are expressed at different developmental stages in Mycobacterium tuberculosis. Sequence analysis shows that the two proteins share 18% amino acid identities and belong to different groups within the truncated Hb cluster. Although a specific defense role against nitrosative stress has been ascribed to trHbN (expressed during the Mycobacterium stationary phase), no clear functions have been recognized for trHbO, which is expressed throughout the Mycobacterium growth phase. The 2.1-A crystal structure of M. tuberculosis cyano-met trHbO shows that the protein assembles in a compact dodecamer. Six of the dodecamer subunits are characterized by a double conformation for their CD regions and, most notably, by a covalent bond linking the phenolic O atom of TyrB10 to the aromatic ring of TyrCD1, in the heme distal cavity. All 12 subunits display a cyanide ion bound to the heme Fe atom, stabilized by a tight hydrogen-bonded network based on the (globin very rare) TyrCD1 and TrpG8 residues. The small apolar AlaE7 residue leaves room for ligand access to the heme distal site through the conventional "E7 path," as proposed for myoglobin. Different from trHbN, where a 20-A protein matrix tunnel is held to sustain ligand diffusion to an otherwise inaccessible heme distal site, the topologically related region in trHbO hosts two protein matrix cavities.

  • Organizational Affiliation

    Department of Physics-National Institute of Physics of Matter, Center for Excellence in Biomedical Research, University of Genoa, Genoa, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin-like protein HbO
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
128Mycobacterium tuberculosisMutation(s): 0 
Find proteins for P9WN23 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WN23 
Go to UniProtKB:  P9WN23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WN23
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
AA [auth C]
BB [auth L]
DA [auth D]
HA [auth E]
JA [auth F]
AA [auth C],
BB [auth L],
DA [auth D],
HA [auth E],
JA [auth F],
NA [auth G],
PA [auth H],
S [auth A],
SA [auth I],
W [auth B],
WA [auth J],
YA [auth K]
C34 H32 Fe N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
BA [auth D]
EA [auth E]
FA [auth E]
KA [auth G]
LA [auth G]
BA [auth D],
EA [auth E],
FA [auth E],
KA [auth G],
LA [auth G],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
QA [auth I],
T [auth B],
TA [auth J],
U [auth B],
UA [auth J],
X [auth C],
Y [auth C],
ZA [auth L]
O4 S
Query on CYN

Download Ideal Coordinates CCD File 
AB [auth L]
CA [auth D]
GA [auth E]
IA [auth F]
MA [auth G]
AB [auth L],
CA [auth D],
GA [auth E],
IA [auth F],
MA [auth G],
OA [auth H],
R [auth A],
RA [auth I],
V [auth B],
VA [auth J],
XA [auth K],
Z [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.11 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.034α = 90
b = 187.034β = 90
c = 274.861γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance