PDBsum entry 1q1f

Oxygen storage/transport

PDB id: 1q1f

Contents

Protein chain

148 a.a. *

Ligands

HEM

Waters ×111

* Residue conservation analysis

PDB id:

1q1f

Name:

Oxygen storage/transport

Title:

Crystal structure of murine neuroglobin

Structure:

Neuroglobin. Chain: a. Engineered: yes. Mutation: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: ngb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

1.50Å R-factor: 0.210 R-free: 0.208

Authors:

B.Vallone,K.Nienhaus,K.Matthes,M.Brunori,G.U.Nienhaus

Key ref:

B.Vallone et al. (2004). The structure of murine neuroglobin: Novel pathways for ligand migration and binding. Proteins, 56, 85-92. PubMed id: 15162488 DOI: 10.1002/prot.20113

Date:

19-Jul-03 Release date: 08-Jun-04

Protein chain

Q9ER97  (NGB_MOUSE) -  Neuroglobin from Mus musculus

Seq: 151 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.7.-.-

DOI no: 10.1002/prot.20113

Proteins 56:85-92 (2004)

PubMed id: 15162488

The structure of murine neuroglobin: Novel pathways for ligand migration and binding.

B.Vallone, K.Nienhaus, M.Brunori, G.U.Nienhaus.

ABSTRACT

Neuroglobin, a recently discovered globin predominantly expressed in neuronal tissue of vertebrates, binds small, gaseous ligands at the sixth coordination position of the heme iron. In the absence of an exogenous ligand, the distal histidine (His64) binds to the heme iron in the ferrous and ferric states. The crystal structure of murine ferric (met) neuroglobin at 1.5 A reveals interesting features relevant to the ligand binding mechanism. Only weak selectivity is observed for the two possible heme orientations, the occupancy ratio being 70:30. Two small internal cavities are present on the heme distal side, which enable the His64(E7) side chain to move out of the way upon exogenous ligand binding. Moreover, a third, huge cavity (volume approximately 290 A3) connecting both sides of the heme, is open towards the exterior and provides a potential passageway for ligands. The CD and EF corners exhibit substantial flexibility, which may assist ligands in entering the protein and accessing the active site. Based on this high-resolution structure, further structure-function studies can be planned to elucidate the role of neuroglobin in physiological responses to hypoxia.

Selected figure(s)

Figure 4.
Figure 4. The different heme conformers of Ngb. Blue: conformer A (70% occupancy). Red: conformer B (30%). Close distances are: Tyr44(CD3) OH to heme propionate O2A = 2.6 Å, heme propionate O2A to Wat3 = 2.7 Å, Lys67(E10) NZ to heme propionate O1A = 2.7 Å.

Figure 6.
Figure 6. Modeling dioxygen binding to the distal site of Ngb. a: The original His64(E7) position ( [1] = 178.1°) overlaps with the first atom of the diatomic ligand (0.28 Å). b: His64(E7) swings towards the interior; at [1] = -72.5°, there are no close contacts of the imidazole side chain with other amino acids or with the bound ligand. c: His64(E7) swings towards the exterior; at [1] = 114.5°, there is a steric clash with O2A of the heme propionate (distance 0.63 Å) and close contact with Tyr44(CD3)-OH (2.14 Å) and Wat3 (1.95 Å).

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 56, 85-92) copyright 2004.

Figures were selected by an automated process.