PDBsum entry 1mz0

Oxygen storage/transport

PDB id: 1mz0

Contents

Protein chain

154 a.a. *

Ligands

SO4 ×2

HEM-CMO

Waters ×143

* Residue conservation analysis

PDB id:

1mz0

Name:

Oxygen storage/transport

Title:

Structure of myoglobin mb-yqr 316 ns after photolysis of carbon monoxide solved from laue data at rt.

Structure:

Myoglobin. Chain: a. Engineered: yes. Mutation: yes

Source:

Physeter catodon. Sperm whale. Organism_taxid: 9755. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.60Å R-factor: 0.150 R-free: 0.173

Ensemble:

2 models

Authors:

D.Bourgeois,B.Vallone,F.Schotte,A.Arcovito,A.E.Miele,G.Sciara, M.Wulff,P.Anfinrud,M.Brunori

Key ref:

D.Bourgeois et al. (2003). Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography. Proc Natl Acad Sci U S A, 100, 8704-8709. PubMed id: 12847289 DOI: 10.1073/pnas.1430900100

Date:

04-Oct-02 Release date: 29-Jul-03

Protein chain

P02185  (MYG_PHYMC) -  Myoglobin from Physeter macrocephalus

Seq: 154 a.a.

Struc: 154 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.1.11.1.- - ?????
• Enzyme class 3: E.C.1.7.-.-

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1073/pnas.1430900100

Proc Natl Acad Sci U S A 100:8704-8709 (2003)

PubMed id: 12847289

Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.

D.Bourgeois, B.Vallone, F.Schotte, A.Arcovito, A.E.Miele, G.Sciara, M.Wulff, P.Anfinrud, M.Brunori.

ABSTRACT

Although conformational changes are essential for the function of proteins, little is known about their structural dynamics at atomic level resolution. Myoglobin (Mb) is the paradigm to investigate conformational dynamics because it is a simple globular heme protein displaying a photosensitivity of the iron-ligand bond. Upon laser photodissociation of carboxymyoglobin Mb a nonequilibrium population of protein structures is generated that relaxes over a broad time range extending from picoseconds to milliseconds. This process is associated with migration of the ligand to cavities in the matrix and with a reduction in the geminate rebinding rate by several orders of magnitude. Here we report nanosecond time-resolved Laue diffraction data to 1.55-A resolution on a Mb mutant, which depicts the sequence of structural events associated with this extended relaxation. Motions of the distal E-helix, including the mutated residue Gln-64(E7), and of the CD-turn are found to lag significantly (100-300 ns) behind local rearrangements around the heme such as heme tilting, iron motion out of the heme plane, and swinging of the mutated residue Tyr-29(B10), all of which occur promptly (< or =3 ns). Over the same delayed time range, CO is observed to migrate from a cavity distal to the heme known to bind xenon (called Xe4) to another such cavity proximal to the heme (Xe1). We propose that the extended relaxation of the globin moiety reflects reequilibration among conformational substates known to play an essential role in controlling protein function.

Selected figure(s)

Figure 1.
Fig. 1. Structural changes in YQR-Mb 316 ns after photolysis. (a) Overlay of (F[light] - F[dark]) difference electron density maps on the YQR-MbCO model (red, negative; green, positive; contoured at 3.5 , where is the standard deviation of the electron density difference). Most changes are clustered on the distal (upper) side of the heme. (b) Overview of the modeled structure of YQR-MbCO (red) and YQR-Mb* (green). The heme and several key residues are rendered as balls and sticks, the CO is rendered as space filling, and the rest of the protein is rendered as ribbon.

Figure 2.
Fig. 2. Detailed view of the time-dependent electron density differences (red, negative; green, positive) overlaid on the models of YQR-MbCO (yellow) and YQR-Mb* (blue). (a) Heme vicinity: the disappearance of bound CO, tilting of the heme, swinging motion of Tyr-29(B10), and migration of photolyzed CO to the Xe4 docking site (orange stick) are fully developed by 3 ns (contoured to 3.0 ); by 316 ns, the photolyzed CO has reached the Xe1 docking site (blue stick). (b) Concerted motion of Asp-60(E3), Phe-46(CD4), and Wat56, reaching a maximum amplitude by 316 ns (contoured to 3.0 ). (c) Overview of structural changes taking place around the E-helix, CD-turn, and F-helix (contoured to 4.0 ).

Figures were selected by an automated process.