PDBsum entry 1v07

Oxygen transport

PDB id: 1v07

Contents

Protein chain

110 a.a. *

Ligands

HEM-OXY

SO4

Waters ×92

* Residue conservation analysis

PDB id:

1v07

Name:

Oxygen transport

Title:

Crystal structure of thre11val mutant of the nerve tissue mini- hemoglobin from the nemertean worm cerebratulus lacteus

Structure:

Neural hemoglobin. Chain: a. Synonym: nrhb. Engineered: yes. Mutation: yes

Source:

Cerebratulus lacteus. Milky ribbon worm. Organism_taxid: 6221. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.170 R-free: 0.195

Authors:

A.Pesce,M.Nardini,P.Ascenzi,E.Geuens,S.Dewilde,L.Moens,M.Bolognesi, A.Riggs,A.Hale,P.Deng,G.U.Nienhaus,J.S.Olson,K.Nienhaus

Key ref:

A.Pesce et al. (2004). Thr-E11 regulates O2 affinity in Cerebratulus lacteus mini-hemoglobin. J Biol Chem, 279, 33662-33672. PubMed id: 15161908 DOI: 10.1074/jbc.M403597200

Date:

24-Mar-04 Release date: 03-Jun-04

Protein chain

O76242  (GLBN_CERLA) -  Neural hemoglobin from Cerebratulus lacteus

Seq: 110 a.a.

Struc: 110 a.a.*

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

DOI no: 10.1074/jbc.M403597200

J Biol Chem 279:33662-33672 (2004)

PubMed id: 15161908

Thr-E11 regulates O2 affinity in Cerebratulus lacteus mini-hemoglobin.

A.Pesce, M.Nardini, P.Ascenzi, E.Geuens, S.Dewilde, L.Moens, M.Bolognesi, A.F.Riggs, A.Hale, P.Deng, G.U.Nienhaus, J.S.Olson, K.Nienhaus.

ABSTRACT

The mini-hemoglobin from Cerebratulus lacteus (CerHb) belongs to a class of globins containing the polar Tyr-B10/Gln-E7 amino acid pair that normally causes low rates of O2 dissociation and ultra-high O2 affinity, which suggest O2 sensing or NO scavenging functions. CerHb, however, has high rates of O2 dissociation (kO2 = 200-600 s(-1)) and moderate O2 affinity (KO2) approximately 1 microm(-1)) as a result of a third polar amino acid in its active site, Thr-E11. When Thr-E11 is replaced by Val, kO2 decreases 1000-fold and KO2 increases 130-fold at pH 7.0, 20 degrees C. The mutation also shifts the stretching frequencies of both heme-bound and photodissociated CO, indicating marked changes of the electrostatic field at the active site. The crystal structure of Thr-E11 --> Val CerHbO2 at 1.70 A resolution is almost identical to that of the wild-type protein (root mean square deviation of 0.12 A). The dramatic functional and spectral effects of the Thr-E11 --> Val mutation are due exclusively to changes in the hydrogen bonding network in the active site. Replacing Thr-E11 with Val "frees" the Tyr-B10 hydroxyl group to rotate toward and donate a strong hydrogen bond to the heme-bound ligand, causing a selective increase in O2 affinity, a decrease of the rate coefficient for O2 dissociation, a 40 cm(-1) decrease in nuCO of heme-bound CO, and an increase in ligand migration toward more remote intermediate sites.

Selected figure(s)

Figure 1.
FIG. 1. a, O[2] rebinding to wild-type CerHb, Thr-E11 Val CerHb, and wild-type sperm whale (sw) Mb at pH 7.0, 20 °C. The concentration of O[2] was 1,250 µM (buffer equilibrated with 1 atm pure O[2]). O[2] displacement from wild-type CerHbO[2], Thr-E11 Val CerHbO[2], and wild-type sperm whale MbO[2] at pH 7.0, 20 °C is shown on short (b) and long (c) time scales.

Figure 2.
FIG. 2. A stereo view of the CerHb heme distal (upper part of the figure) and proximal sites (lower part, hosting His-F8). Short fragments of the B- and E-helices are displayed as cyan ribbons. The heme is shown in red. The relevant residues are displayed with light gray bonds, using black labels for the wild-type CerHb structure. Structural modifications observed in the Thr-E11 Val CerHb mutant are highlighted by displaying residues Tyr-B10 and Val E11 in orange. The dashed arrows indicate hydrogen bond donation in the wild-type protein (blue arrows) and in the Thr-E11 Val mutant (orange arrow). The O[2] molecule is displayed at the sixth coordination site of the heme iron as a purple diatomic species (partly covered by arrows). Lys-E10 is electrostatically coupled to both heme propionates and contributes to the shielding of the distal heme pocket.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 33662-33672) copyright 2004.

Figures were selected by an automated process.